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

NucPred

Fetching P32874 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  KGKTITHGQSWGARRIHSHFYITIFTITCIRIGQYKLALYLDPYRFYNIT    50
  51  GSQIVRLKGQRPEYRKRIFAHSYRHSSRIGLNFPSRRRYSNYVDRGNIHK   100
 101  HTRLPPQFIGLNTVESAQPSILRDFVDLRGGHTVISKILIANNGIAAVKE   150
 151  MRSIRKWAYETFNDEKIIQFVVMATPDDLHANSEYIRMADQYVQVPGGTN   200
 201  NNNYANIDLILDVAEQTDVDAVWAGWGHASENPCLPELLASSQRKILFIG   250
 251  PPGRAMRSLGDKISSTIVAQSAKIPCIPWSGSHIDTIHIDNKTNFVSVPD   300
 301  DVYVRGCCSSPEDALEKAKLIGFPVMIKASEGGGGKGIRRVDNEDDFIAL   350
 351  YRQAVNETPGSPMFVMKVVTDARHLEVQLLADQYGTNITLFGRDCSIQRR   400
 401  HQKIIEEAPVTITKPETFQRMERAAIRLGELVGYVSAGTVEYLYSPKDDK   450
 451  FYFLELNPRLQVEHPTTEMISGVNLPATQLQIAMGIPMHMISDIRKLYGL   500
 501  DPTGTSYIDFKNLKRPSPKGHCISCRITSEDPNEGFKPSTGKIHELNFRS   550
 551  SSNVWGYFSVGNNGAIHSFSDSQFGHIFAVGNDRQDAKQNMVLALKDFSI   600
 601  RGEFKTPIEYLIELLETRDFESNNISTGWLDDLILKNLSSDSKLDPTLAI   650
 651  ICGAAMKAYVFTEKVRNKYLELLRRGQVPPKDFLKTKFPVDFIFDNNRYL   700
 701  FNVAQSSEEQFILSINKSQCEVNVQKLSSDCLLISVDGKCHTVYWKDDIR   750
 751  GTRLSIDSNTIFLEAELNPTQVISPTPGKLVKYLVRSGDHVFAGQQYAEI   800
 801  EIMKMQMPLVAKSDGVIELLRQPGSIIEAGDVIAKLTLDSPSKANESSLY   850
 851  RGELPVLGPPLIEGSRPNHKLRVLINRLENILNGYHENSGIETTLKELIK   900
 901  ILRDGRLPYSEWDSQISTVRNRLPRQLNEGLGNLVKKSVSFPAKELHKLM   950
 951  KRYLEENTNDHVVYVALQPLLKISERYSEGLANHECEIFLKLIKKYYAVE  1000
1001  KIFENHDIHEERNLLNLRRKDLTNLKKILCISLSHANVVAKNKLVTAILH  1050
1051  EYEPLCQDSSKMSLKFRAVIHDLASLESKWAKEVAVKARSVLLRGIFPPI  1100
1101  KKRKEHIKTLLQLHIKDTGAENIHSRNIYSCMRDFGNLIHSNLIQLQDLF  1150
1151  FFFGHQDTALSSIASEIYARYAYGNYQLKSIKIHKGAPDLLMSWQFSSLR  1200
1201  NYLVNSDGESDEFTKLSKPPSTSGKSSANSFGLLVNMRALESLEKTLDEV  1250
1251  YEQIHIPEERLSSGENSLIVNILSPIRYRSENDLIKTLKIKLHENERGLS  1300
1301  KLKVNRITFAFIAANAPAVKFYSFDGTTYDEISQIRNMDPSYEAPLELGK  1350
1351  MSNYKIRSLPTYDSSIRIFEGISKFTPLDKRFFVRKIINSFMYNDQKTTE  1400
1401  ENLKAEINAQVVYMLEHLGAVDISNSDLNHIFLSFNTVLNIPVHRLEEIV  1450
1451  STILKTHETRLFQERITDVEICISVECLETKKPAPLRLLISNKSGYVVKI  1500
1501  ETYYEKIGKNGNLILEPCSEQSHYSQKSLSLPYSVKDWLQPKRYKAQFMG  1550
1551  TTYVYDFPGLFHQAAIQQWKRYFPKHKLNDSFFSWVELIEQNGNLIKVNR  1600
1601  EPGLNNIGMVAFEIMVQTPEYPEGRNMIVISNDITYNIGSFGPREDLFFD  1650
1651  RVTNYARERGIPRIYLAANSGAKLGIAEELIPLFRVAWNDPSDPTKGFQY  1700
1701  LYLAPKDMQLLKDSGKGNSVVVEHKMVYGEERYIIKAIVGFEEGLGVECL  1750
1751  QGSGLIAGATSKAYRDIFTITAVTCRSVGIGSYLVRLGQRTIQVEDKPII  1800
1801  LTGASAINKVLGTDIYTSNLQIGGTQIMYKNGIAHLTASNDMKAIEKIMT  1850
1851  WLSYVPAKRDMSPPLLETMDRWDRDVDFKPAKQVPYEARWLIEGKWDSNN  1900
1901  NFQSGLFDKDSFFETLSGWAKGVIVGRARLGGIPVGVIAVETKTIEEIIP  1950
1951  ADPANLDSSEFSVKEAGQVWYPNSAFKTAQTINDFNYGEQLPLIILANWR  2000
2001  GFSGGQRDMYNEVLKYGSFIVDALVDYKQPILIYIPPFGELRGGSWVVID  2050
2051  PTINPEQMEMYADVESRGGVLEPDGVVSIKYRKEKMIETMIRLDSTYGHL  2100
2101  RRTLTEKKLSLEKQNDLTKRLKIRERQLIPIYNQISIQFADLHDRSTRML  2150
2151  VKGVIRNELEWKKSRRFLYWRLRRRLNEGQVIKRLQKKTCDNKTKMKYDD  2200
2201  LLKIVQSWYNDLDVNDDRAVVEFIERNSKKIDKNIEEFEISLLIDELKKK  2250
2251  FEDRRGNIVLEELTRLVDSKRKR                             2273

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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