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

NucPred

Fetching Q85FR6 from www.uniprot.org...

The NucPred score for your sequence is 0.43 (see score help below)

   1  MCDAIQIRLASPERIRSWAERVLPNGQVVGEVTKPETINYRTLKPEMDGL    50
  51  FCERIFGPVKDWECHCGKYKKVRYKGIVCERCGVEVTESKVRRHRMGYID   100
 101  LAAVVSHVWYLKGPPSYLALFLNMSSSEVEQVIYFHSYVVLQSTTELVQP   150
 151  KQLLSEDELIILEERLANQPFQVGIGAQAIQYLLQQLDLDMEIRVLRNQL   200
 201  FHAKSSKREKLMKRLRILDNFASTGADPSWMILSVLPVIPPDLRPMVQLD   250
 251  GGRFATSDLNDLYRRVINRNNRLKRLQEILAPEIIIRNEKRMLQEAVDAL   300
 301  MDNGRRGRSVVGANNRALKSLSHILEGKQGRFRQNLLGKRVDYSGRSVIV   350
 351  VGPELKLYQCGLPKEMALELFQPFVIQRLMAQGLANNMKAAKKIIQRKEA   400
 401  IVDQILHQVVKAHPVLLNRAPTLHRLGIQAFDPILVDGRAIQLHPLVCAA   450
 451  FNADFDGDQMAVHVPLSVEAQAEARLLMLSVNNFLSPATGDAIIMPSQDM   500
 501  VIGCYYLTANNPASQAKQSHYFADFEHVLMAFEQKQINLHTWVWVHVNNN   550
 551  LNIILERSALQEDWIQTRGESLFLKTTPGRIIFYQQAAYHVGFYNLTINK   600
 601  SHLKELVKTVYNLKGMACATQLADDLKQLGFHYATTCGLSLGIEDLRVAP   650
 651  SKQKIFQWAQQAIEKTEQLWQRAQITHVEKFHKVVDTWSEASETLKQEVV   700
 701  RYYEHTDPLNPVYMMAFSGARGNLSQVRQLVGMRGLMADPHGQLIDLPIL   750
 751  SNFREGLTVTEYLISSYGARKGLVDTSLRTADSGYLTRRLVDVAQDVIIR   800
 801  QADCGTLRGIAVPVSKALIGRVLAQDVNEECKRNQLITADMLVALRDTKQ   850
 851  VIVRSPLTCEALRCICQLCYGGNLAYGHMVDLAEAVGIIAAQSIGEPGTQ   900
 901  LTMRTFHTGGVFTSAQTASVRATLDGVVTYEGRCKSTRTRYGQEAWLLET   950
 951  STPLFLQNDGQQHRYDFQAGTVLLVKSGQRVKFNTLLAYLPTSTRFEKAT  1000
1001  KSVDAHNAGEVVFDQLKLEQNLVKKEGILWILSGQMLHLPAGSELLVSNE  1050
1051  QQIKPAQVLAQSYLRSRAKGIVQIHTNQVELILDRLSFEVKEPFHFHSGD  1100
1101  GQIIAEKFEHQTPTGGQVFHRNGQIWLVPAAIYEVSSQKDLVDIKHGQFI  1150
1151  LANQRSICGVKNELSGWVQLVKQNEVIKEIRIRPGIYLPKVKTNQLGFVQ  1200
1201  SHLLLSSYGINAYTRRFCYVENYEQGILISPVYVFAGVSPPKIVAKSRWL  1250
1251  SLVMYQTCMFQHQQWVKSYKKVYLMRCQLQLKVAPQAPLNQVTVHKEKNR  1300
1301  REWRLSYFSNIKLQAFQTIKWLVKNHQRVEADVPLALIQLVSAFNGIVRY  1350
1351  HPMLNRLLVVSDQDVITYSIGKPHHFQIGDVIRIGDQISHGLVAKTSGFV  1400
1401  IARDANQIQVRIAQGYFLSRETICYVKDGDLVNEGDHLASLVFEQVKTGD  1450
1451  IIQGLPRIEEILEARKPKNSCELAQFDGVIQEQSLVSDDGRVQAIKGTLI  1500
1501  VCEGTRVQAGEPLTDGAVNAHEWLQIHFNNAVPYRGMVEAARESFAKLQA  1550
1551  KLLHQVQQVYKSQGVDIADKHIEVILRQMTSKVILDDPGDSDFLPGQLVY  1600
1601  LNEIASYKHVIFHPVLLGITKAALNTESFISAASFQETTRILAQAAMEGQ  1650
1651  IDQLRGLKENVIMGRLIPAGTGAKYL                          1676

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.)

Go back to the NucPred Home Page.