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

NucPred

Fetching P12276 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MEDVVIAGIAGKLPESENLQEFWENLLNGVDMVTEDDRRWKPGIYGLPKR    50
  51  NGKLKDIKKFDASFFGVHPKQAHTMDPQLRLLLEVSYEAILDGGINPTAL   100
 101  RGTDTGVWVGASGSEALEALSQDPEELLGYSMTGCQRAMLANRISYFYDF   150
 151  TGPSLTIDTACSSSLMALENAYKAIRHGQCSAALVGGVNILLKPNTSVQF   200
 201  MKLGMLSPDGACKAFDVSGNGYCRSEAVVVVLLTKKSMAKRVYATIVNAG   250
 251  SNTDGFKEQGVTFPSGEMQQQLVGSLYRECGIKPGDVEYVEAHGTGTKVG   300
 301  DPQEVNGIVNVFCQCEREPLLIGSTKSNMGHPEPASGLAALAKVILSLEH   350
 351  GLWAPNLHFNDPNPDIPALHDGSLKVVCKPTPVKGGLVSINSFGFGGSNA   400
 401  HVILRPNEKKCQPQETCNLPRLVQVCGRTQEAVEILIEESRKHGGCSPFL   450
 451  SLLSDISAVPVSSMPYRGYTLVGTESDITEIQQVQASGRPLWYICSGMGT   500
 501  QWKGMGLSLMKLDLFRQSILRSDEALKSTGLKVSDLLLNADENTFDDTVH   550
 551  AFVGLAAIQIAQIDVLKAAGLQPDGILGHSVGELACGYADNSLSHEEAVL   600
 601  AAYWRGRCVKEAKLPPGGMAAVGLTWEECKQRCPPNVVPACHNSEDTVTV   650
 651  SGPLDSVSEFVTKLKKDGVFAKEVRRAGVAFHSYYMASIAPALLSALKKV   700
 701  IPHPKPRSARWISTSIPESQWQSDLARNSSAEYHVNNLVNPVLFHEGLKH   750
 751  IPENAVVVEIAPHALLQAILRRTLKPTCTILPLMKKDHKNNLEFFLTQTG   800
 801  KIHLTGINVLGNNLFPPVEYPVPVGTPLISPYIKWDHSQDWDVPKAEDFP   850
 851  SGSKGSASASVYNIDVSPDSPDHYLVGHCIDGRVLYPATGYLVLAWRTLA   900
 901  RSLGMVMEQTAVMFEEVTIHQATILPKKGSTQLEVRIMPASHSFEVSGNG   950
 951  NLAVSGKISLLENDALKNFHNQLADFQSQANVTAKSGLLMEDVYQELHLR  1000
1001  GYNYGPTFQGVLECNSEGSAGKILWNGNWVTFLDTLLHLIVLAETGRSLR  1050
1051  LPTRIRSVYIDPVLHQEQVYQYQDNVEAFDVVVDRCLDSLKAGGVQINGL  1100
1101  HASVAPRRQQERISPTLEKFSFVPYIESDCLSSSTQLHAYLEHCKGLIQK  1150
1151  LQAKMALHGVKLVIHGLETKGAAAGSPPAQKGLQHILTEICRLELNGNPH  1200
1201  SELEQIVTQEKMHLQDDPLLNGLLDSSELKTCLDVAKENTTSHRMKIVEA  1250
1251  LAGSGRLFSRVQSILNTQPLLQLDYIATDCTPETLSDNETELHDAGISFS  1300
1301  QWDPSSLPSGNLTNADLAVCNCSTSVLGNTAEIISNLAAAVKEGGFVLLH  1350
1351  TLLKEETLGEIVSFLTSPDLQQKHSFLSQAQWEELFSKASLNLVAMKRSF  1400
1401  FGSVIFLCRRQSPAKAPILLPVDDTHYKWVDSLKEILADSSEQPLWLTAT  1450
1451  NCGNSGILGMVNCLRLEAEGHRIRCVFVSNLSPSSTVPATSLSSLEMQKI  1500
1501  IERDLVMNVYRDGKWGSFRHLPLQQAQPQELTECAYVNVLTRGDLSSLRW  1550
1551  IVSPLRHFQTTNPNVQLCKVYYASLNFWDIMLATGKLSPDAIPGNWTLQQ  1600
1601  CMLGMEFSGRDLAGRRVMGLLPAKGLATVVDCDKRFLWEVPENWTLEEAA  1650
1651  SVPVVYATAYYALVVRGGMKKGESVLIHSGSGGVGQAAIAIALSMGCRVF  1700
1701  ATVGSAEKREYLQARFPQLDANSFASSRNTTFQQHILRVTNGKGVSLVLN  1750
1751  SLAEEKLQASLRCLAQHGRFLEIGKFDLSNNSQLGMALFLKNVAFHGILL  1800
1801  DSIFEEGNQEWEVVSELLTKGIKDGVVKPLRTTVFGKEEVEAAFRFMAQG  1850
1851  KHIGKVMIKIQEEEKQYPLRSEPVKLSAISRTSCPPTKSYIITGGLGGFG  1900
1901  LELAQWLIERGAQKLVLTSRSGIRTGYQAKCVREWKALGIQVLVSTSDVG  1950
1951  TLEGTQLLIEEALKLGPVGGIFNLAVVLKDAMIENQTPELFWEVNKPKYS  2000
2001  GTLHLDWVTRKKCPDLDYFVVFSSVSCGRGNAGQSNYGFANSAMERICEQ  2050
2051  RHHDGLPGLAVQWGAIGDVGILKAMGNREVVIGGTVLQQISSCLEVLDMF  2100
2101  LNQPHPVMSSFVLAEKVSVKSEGGSQRDLVEAVAHILGVRDVSSLNAESS  2150
2151  LADLGLDSLMGVEVRQTLERDYDIVMTMREIRLLTINKLRELSSKTGTAE  2200
2201  ELKPSQVLKTGPGEPPKLDLNNLLVNPEGPTITRLNEVQSTERPLFLVHP  2250
2251  IEGSIAVFYTLASKLHMPCYGLQCTKAAPLDSIQSLASYYIDCMKQIQPE  2300
2301  GPYRIAGYSFGACVAFEMCSQLQAQQNASHALNSLFLFDGSHSFVAAYTQ  2350
2351  SYRAKLTQGNEAALETEALCAFVQQFTGIEYNKLLEILLPLEDLEARVNA  2400
2401  AADLITQIHKNINREALSFAAASFYHKLKAADKYIPESKYHGNVTLMRAK  2450
2451  THNEYEEGLGGDYRLSEVCDGKVSVHIIEGDHRTLLEGDGVESIIGIIHG  2500
2501  SLAEPRVSVREG                                        2512

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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