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

NucPred

Fetching Q6BN88 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MLPKEDKVNSNHFKGVNDAHKTSLYKRLSSSVIPPLTFLNQNPASPNNEE    50
  51  VPGNNEANKDEKTFSDDEDIAHPIGSVGSSNNFLSFLYAGMGKLSDLKGN   100
 101  DASNANEAKDSKLNDNLRSSRNEQANEPEYRREYKLDYDIDESEEDDIES   150
 151  TRDENTLKPKTEDTSVHSKLDPEERLENVVNMLFDDHDESTTALASDPSK   200
 201  GTVFQQSVLKNFDPFRIQQTELLKLKDITLSTEEDESEEQKLKKKFFRLK   250
 251  VADKLKRVFELNDDDYFYGNYNVWLVRDVLLQGHIYLTKESILFFTFLPK   300
 301  RHNTISASKGTTGGFQHHDDSHDVIQSGSLGMKTALYGDTVFSTPLTHRF   350
 351  WVILRNETITVYHSPTDLYFPITLIDLKSCVRAEVIEKGRNDNASPRPDL   400
 401  HRNDSQEVSSGDEEVEFSNMLNSNYQLEDNSENVSGGYWFKVVTKKKTHK   450
 451  FHSDSLYSARQWVNNIVKVVFQLHNSNANNEVIMKIPINDVLSFDLNEVF   500
 501  GASEKNSDSNGGEEKPKVLNVKYLENGSKGRYALSASRMKKELKNKTKKK   550
 551  MKKNSGNEPDELLSENTYFLLFKDGDEVFSTLNEIVNENHHSSNIFRNRH   600
 601  NSISKKYTSEKGSNWNRPFTHKDEEIHIPRAISTLTTDHFQNSIIDQIEE   650
 651  ASHRNTHTQNTDLASPRSECGLTHSVSTSPQSKIRKFGKTLITPSKIFSN   700
 701  KSRTESEKSTPDRSQTTSPVQGINLSLSGLKDLNMAFEASQKNYEVSCTR   750
 751  YSHTEENSTNSPSNFQNNTLSKADALSPQIKSPQPLEAGPLNLTDPSEYE   800
 801  DNKKKNSTLSSIGKSIKAMSSIRSKLAAVNHYEQLDENDTYFIRDVSARE   850
 851  VDTRHFQERFSFNNKKQLIASYHCHIIRAVPVFGKVYLGDSEICFRSMLP   900
 901  GVSTRMILPLIDVDTCSKEKGSNIAYSGLVLVIRGYDELFMEFSVQSARD   950
 951  DCLAMILRQLEKNRESGNESSDDNKSAQHGKSGCFQKTPSSAETTKSSNE  1000
1001  IKLAQWRIENARLKLFEDKINAAAGLHVPIVLEDSPFYKTEIRPSTSFNF  1050
1051  TLLTIGSRGDVQPYIALGKGLLNEGHNVTIATHSDFEEWIVGHGIKFKTI  1100
1101  AGNPVELMSLMVTHGSMSLSFLKEASSKFRGWIQELLDTSWKACQGSDIL  1150
1151  IESPSAMVGAHIAEALGIPYIRAFTMPWTRTRAYPHAFIVPDKKKGGSYN  1200
1201  YITHLMFETVLWKGISSQVNKWRRESLGLPRTNLYRLAQYDIPFLYNISP  1250
1251  TIFPPSVDFPDWVKVTGYWFLDEGAADDFEPSKELVEFMNKARADDKKVV  1300
1301  YIGFGSIVVEDAKSLTKAIVEAVLNADVRCILNKGWSDRNSSPAKDNAEP  1350
1351  EVELPEEIYNSGSIPHDWLFPKIDAAVHHGGSGTTGATMRAGIPTIIKPF  1400
1401  FGDQFFYSSRIEDIGAGIGLKKLNARSLCTALKTATSDAKMITKAKKISE  1450
1451  RLKQENGVLNAIEAIYYELEYARSLILAKQHENTKHDLKSGTQTPVVNET  1500
1501  NEYFDSDTYDADHDSDKESDHDQTYEQDNHSDYDVANDDNMTEIVEPSLE  1550
1551  DGNDTVRIAPDSGNDNTTVTDANK                            1574

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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