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

NucPred

Fetching Q13402 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MVILQQGDHVWMDLRLGQEFDVPIGAVVKLCDSGQVQVVDDEDNEHWISP    50
  51  QNATHIKPMHPTSVHGVEDMIRLGDLNEAGILRNLLIRYRDHLIYTYTGS   100
 101  ILVAVNPYQLLSIYSPEHIRQYTNKKIGEMPPHIFAIADNCYFNMKRNSR   150
 151  DQCCIISGESGAGKTESTKLILQFLAAISGQHSWIEQQVLEATPILEAFG   200
 201  NAKTIRNDNSSRFGKYIDIHFNKRGAIEGAKIEQYLLEKSRVCRQALDER   250
 251  NYHVFYCMLEGMSEDQKKKLGLGQASDYNYLAMGNCITCEGRVDSQEYAN   300
 301  IRSAMKVLMFTDTENWEISKLLAAILHLGNLQYEARTFENLDACEVLFSP   350
 351  SLATAASLLEVNPPDLMSCLTSRTLITRGETVSTPLSREQALDVRDAFVK   400
 401  GIYGRLFVWIVDKINAAIYKPPSQDVKNSRRSIGLLDIFGFENFAVNSFE   450
 451  QLCINFANEHLQQFFVRHVFKLEQEEYDLESIDWLHIEFTDNQDALDMIA   500
 501  NKPMNIISLIDEESKFPKGTDTTMLHKLNSQHKLNANYIPPKNNHETQFG   550
 551  INHFAGIVYYETQGFLEKNRDTLHGDIIQLVHSSRNKFIKQIFQADVAMG   600
 601  AETRKRSPTLSSQFKRSLELLMRTLGACQPFFVRCIKPNEFKKPMLFDRH   650
 651  LCVRQLRYSGMMETIRIRRAGYPIRYSFVEFVERYRVLLPGVKPAYKQGD   700
 701  LRGTCQRMAEAVLGTHDDWQIGKTKIFLKDHHDMLLEVERDKAITDRVIL   750
 751  LQKVIRGFKDRSNFLKLKNAATLIQRHWRGHNCRKNYGLMRLGFLRLQAL   800
 801  HRSRKLHQQYRLARQRIIQFQARCRAYLVRKAFRHRLWAVLTVQAYARGM   850
 851  IARRLHQRLRAEYLWRLEAEKMRLAEEEKLRKEMSAKKAKEEAERKHQER   900
 901  LAQLAREDAERELKEKEAARRKKELLEQMERARHEPVNHSDMVDKMFGFL   950
 951  GTSGGLPGQEGQAPSGFEDLERGRREMVEEDLDAALPLPDEDEEDLSEYK  1000
1001  FAKFAATYFQGTTTHSYTRRPLKQPLLYHDDEGDQLAALAVWITILRFMG  1050
1051  DLPEPKYHTAMSDGSEKIPVMTKIYETLGKKTYKRELQALQGEGEAQLPE  1100
1101  GQKKSSVRHKLVHLTLKKKSKLTEEVTKRLHDGESTVQGNSMLEDRPTSN  1150
1151  LEKLHFIIGNGILRPALRDEIYCQISKQLTHNPSKSSYARGWILVSLCVG  1200
1201  CFAPSEKFVKYLRNFIHGGPPGYAPYCEERLRRTFVNGTRTQPPSWLELQ  1250
1251  ATKSKKPIMLPVTFMDGTTKTLLTDSATTAKELCNALADKISLKDRFGFS  1300
1301  LYIALFDKVSSLGSGSDHVMDAISQCEQYAKEQGAQERNAPWRLFFRKEV  1350
1351  FTPWHSPSEDNVATNLIYQQVVRGVKFGEYRCEKEDDLAELASQQYFVDY  1400
1401  GSEMILERLLNLVPTYIPDREITPLKTLEKWAQLAIAAHKKGIYAQRRTD  1450
1451  AQKVKEDVVSYARFKWPLLFSRFYEAYKFSGPSLPKNDVIVAVNWTGVYF  1500
1501  VDEQEQVLLELSFPEIMAVSSSRECRVWLSLGCSDLGCAAPHSGWAGLTP  1550
1551  AGPCSPCWSCRGAKTTAPSFTLATIKGDEYTFTSSNAEDIRDLVVTFLEG  1600
1601  LRKRSKYVVALQDNPNPAGEESGFLSFAKGDLIILDHDTGEQVMNSGWAN  1650
1651  GINERTKQRGDFPTDSVYVMPTVTMPPREIVALVTMTPDQRQDVVRLLQL  1700
1701  RTAEPEVRAKPYTLEEFSYDYFRPPPKHTLSRVMVSKARGKDRLWSHTRE  1750
1751  PLKQALLKKLLGSEELSQEACLAFIAVLKYMGDYPSKRTRSVNELTDQIF  1800
1801  EGPLKAEPLKDEAYVQILKQLTDNHIRYSEERGWELLWLCTGLFPPSNIL  1850
1851  LPHVQRFLQSRKHCPLAIDCLQRLQKALRNGSRKYPPHLVEVEAIQHKTT  1900
1901  QIFHKVYFPDDTDEAFEVESSTKAKDFCQNIATRLLLKSSEGFSLFVKIA  1950
1951  DKVLSVPENDFFFDFVRHLTDWIKKARPIKDGIVPSLTYQVFFMKKLWTT  2000
2001  TVPGKDPMADSIFHYYQELPKYLRGYHKCTREEVLQLGALIYRVKFEEDK  2050
2051  SYFPSIPKLLRELVPQDLIRQVSPDDWKRSIVAYFNKHAGKSKEEAKLAF  2100
2101  LKLIFKWPTFGSAFFEVKQTTEPNFPEILLIAINKYGVSLIDPKTKDILT  2150
2151  THPFTKISNWSSGNTYFHITIGNLVRGSKLLCETSLGYKMDDLLTSYISQ  2200
2201  MLTAMSKQRGSRSGK                                     2215

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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