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

NucPred

Fetching Q8WZ74 from www.uniprot.org...

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

   1  MATDGASCEPDLSRAPEDAAGAAAEAAKKEFDVDTLSKSELRMLLSVMEG    50
  51  ELEARDLVIEALRARRKEVFIQERYGRFNLNDPFLALQRDYEAGAGDKEK   100
 101  KPVCTNPLSILEAVMAHCKKMQERMSAQLAAAESRQKKLEMEKLQLQALE   150
 151  QEHKKLAARLEEERGKNKQVVLMLVKECKQLSGKVIEEAQKLEDVMAKLE   200
 201  EEKKKTNELEEELSAEKRRSTEMEAQMEKQLSEFDTEREQLRAKLNREEA   250
 251  HTTDLKEEIDKMRKMIEQLKRGSDSKPSLSLPRKTKDRRLVSISVGTEGT   300
 301  VTRSVACQTDLVTENADHMKKLPLTMPVKPSTGSPLVSANAKGSVCTSAT   350
 351  MARPGIDRQASYGDLIGASVPAFPPPSANKIEENGPSTGSTPDPTSSTPP   400
 401  LPSNAAPPTAQTPGIAPQNSQAPPMHSLHSPCANTSLHPGLNPRIQAARF   450
 451  RFQGNANDPDQNGNTTQSPPSRDVSPTSRDNLVAKQLARNTVTQALSRFT   500
 501  SPQAGAPSRPGVPPTGDVGTHPPVGRTSLKTHGVARVDRGNPPPIPPKKP   550
 551  GLSQTPSPPHPQLKVIIDSSRASNTGAKVDNKTVASTPSSLPQGNRVINE   600
 601  ENLPKSSSPQLPPKPSIDLTVAPAGCAVSALATSQVGAWPAATPGLNQPA   650
 651  CSDSSLVIPTTIAFCSSINPVSASSCRPGASDSLLVTASGWSPSLTPLLM   700
 701  SGGPAPLAGRPTLLQQAAAQGNVTLLSMLLNEEGLDINYSCEDGHSALYS   750
 751  AAKNGHTDCVRLLLSAEAQVNAADKNGFTPLCAAAAQGHFECVELLISYD   800
 801  ANINHAADGGQTPLYLACKNGNKECIKLLLEAGTNRSVKTTDGWTPVHAA   850
 851  VDTGNVDSLKLLMYHRIPAHGNSFNEEESESSVFDLDGGEESPEGISKPV   900
 901  VPADLINHANREGWTAAHIAASKGFKNCLEILCRHGGLEPERRDKCNRTV   950
 951  HDVATDDCKHLLENLNALKIPLRISVGEIEPSNYGSDDLECENTICALNI  1000
1001  RKQTSWDDFSKAVSQALTNHFQAISSDGWWSLEDVTCNNTTDSNIGLSAR  1050
1051  SIRSITLGNVPWSVGQSFAQSPWDFMRKNKAEHITVLLSGPQEGCLSSVT  1100
1101  YASMIPLQMMQNYLRLVEQYHNVIFHGPEGSLQDYIVHQLALCLKHRQMA  1150
1151  AGFSCEIVRAEVDAGFSKEQLLDLFISSACLIPVKQSPSKKKIIIILENL  1200
1201  EKSSLSELLRDFLAPLENRSTESPCTFQKGNGLSECYYFHENCFLMGTIA  1250
1251  KACLQGSDLLVQQHFRWVQLRWDGEPMQGLLQRFLRRKVVNKFKGQAPSP  1300
1301  CDPVCKIVDWALSVWRQLNSCLARLGTPEALLGPKYFLSCPVVPGHAQVT  1350
1351  VKWMSKLWNGVIAPRVQEAILSRASVKRQPGFGQTTAKRHPSQGQQAVVK  1400
1401  AALSILLNKAVLHGCPLPRAELDQHTADFKGGSFPLSIVSSYNTCNKKKG  1450
1451  ESGAWRKVNTSPRRKSGRFSLPTWNKPDLSTEGMKNKTISQLNCNRNASL  1500
1501  SKQKSLENDLSLTLNLDQRLSLGSDDEADLVKELQSMCSSKSESDISKIA  1550
1551  DSRDDLRMFDSSGNNPVLSATINNLRMPVSQKEVSPLSSHQTTECSNSKS  1600
1601  KTELGVSRVKSFLPVPRSKVTQCSQNTKRSSSSSNTRQIEINNNSKEVNW  1650
1651  NLHKNEHLEKPNK                                       1663

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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