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

NucPred

Fetching P25823 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MNGQARIALPSKVDLYITHVDHVGPYLKVYGHVNRDAASLISERIRNLLP    50
  51  TCFAIEPSWSVERQQALLIPGTFCIFKNINGPAPGDVEYRRIRVVSADLE   100
 101  GQSMRAEIDFVDFGYKRTVDSHDLMFPKQPKLLQNIPLHCFQYIVLGICS   150
 151  EWDQTDLAEVRRLVVNQIVKITVEPTQICDQKFASLRWKDFELNEFLVQQ   200
 201  KQIGVSVDKQLMMDHCKKLWKDNPQSPVTEYNNNSIHNSKTPMEIAREQL   250
 251  AVRQSLAARLDAQRSVQVTPSRPLNADAPDYTPKHLPLVNVTNVQVQMPG   300
 301  LNNTQKPVFVSTNPYNRANYQPAVPAAQPYVPKANPRSQYTYYNVRMNKP   350
 351  INAMPPPAGPHVPIQHFNQQANNVSLSYVPARFTPPPTPSIAQHQIPIPA   400
 401  FRTTSLTVGLTYDVVISYVENGPYLFWVHLKSSDHDLSTMMGQIERTKLK   450
 451  ALAQAPELGTACVARFSEDGHLYRAMVCAVYAQRYRVVYVDYGNSELLSA   500
 501  SDLFQIPPELLEIKPFAFRFALAGTKEIEPIDDSMKRIFKKSAIYRNFEL   550
 551  TVQAPESVGSMQTCHLNQNGTNMLELLRQLKNSRQSYKKAEQLENDDAVE   600
 601  IRFIDSPSNFYVQKVANIGKFEQLMDEMFSYYNANQRVPDQLILGAPCIV   650
 651  KCDQEWYRAEILRVDDSVIVRHVDFGYEQNVKRHLIGHIAEKHLEMPRQA   700
 701  IKCCLKGFENSELSEDKITDQFEMLAEESNIRRRTFSVRIFRIEPDGLNV   750
 751  VNLLAKNLNVMKKLYKLSMPFEQYLSLEKGQFNANNTRAESVISSELNKS   800
 801  HILNSTSIGETENRLQEQEKEQQQKKVDVRQQQLAVEIPQAVKSVSGSKN   850
 851  STDWDKRSSTSAGSKDSKRQQQQQIQRIDRHLDFSCETQSTGSYSSGMSS   900
 901  PRKGNRQQNGRTPIQSPRHNEKQEAKKNARFSNSESPRRSRDGQQGNQRS   950
 951  QNAPQGYAQKPQRQKSTLDGNISSKRSSGVGSDIASSSSESVAAAKPEKY  1000
1001  VSLDKPYALQEMKTPSKEAASLSWWLSPFQFYIVPKSVSAKYDNIMRDMR  1050
1051  EFYRQKQHQPLQLKVGSTVVVRQRKDNAILRATVTACNHMMRKYRVFCVD  1100
1101  TGSLITVTSEDIWQLEQRFADPPCMAHRCSFHSVVTNYDPLYIVDRMETF  1150
1151  VPVNAKVDCEFVSKEKSNQGSNTSSTCSYTVNIFVNGASLRDMLVKAEFL  1200
1201  TEVAPEIRVNLLAGQQIRGKFTSIRDMTSFKVQFDYGNNVNFLCTYDDAK  1250
1251  FVKSNPNLARRFKEFYEGKSFALNVKNVCENNIVHLRPVMPLFMEDRRSF  1300
1301  ICPYPVVLSSFQALVVYTAKPYRVYVQPQAIVPSMQTLLDNMYEHYKAKG  1350
1351  DSLKKFDVGQICAVRSSDGNWYRARISGKDSNAACFEVFYIDYGNTEEIK  1400
1401  RDDIKALDAKFYEHASGFAVEINLPIGRPSNDTKLKARISEILEEKVVTI  1450
1451  KSIEVRRSHLIADVILENNQSVIDLLKAEKLVPGKDLDYMRKQMEKGKSR  1500
1501  TYEYIETVDLTLDEEEDKGRKETVSKSGSANASPKKKQHNDKDREPKKSK  1550
1551  PAEPARTVAPQPVALKTPSPVPAEPAPVPKPATPVPEVVEVPEINPTVRE  1600
1601  AAAESKQAPAQEDPYKDLDCVVLSHCDNPAQFYVHPIDQLSKLNQLHENL  1650
1651  QIVSPSLPQLMNVVNGADCVSMYSVDKCWYRAKIIDAELMVLLFIDYGNT  1700
1701  DCVSDATDIKESMWSHIEPFCLPCALPIRPKGTADWVDAANGIFNESYSK  1750
1751  VPRLEYLTQGDHYTTSYVNMYIDGEDVAKKLIADGFARPLEYLASGCSCY  1800
1801  ISHVNGICDFFIQLERDSKALELIELYLRKKDTLKPLEGFEKGLIVAALF  1850
1851  EDDELWYRAQLQKELPDSRYEVLFIDYGNTSTTSKCLMLSEEIASLPSLS  1900
1901  KKCSLQLPDAYISWSPEAEAKFAELTGEGELVFTTQLLKPGQDHVTIDLL  1950
1951  LDGENIIDRLLPLCQRKEPKEASKESLAVTTKAIITHVENTSRIYLQFSE  2000
2001  KDSLMDIICEKLNGSKLQPKTEKAAVDDMCVVQFADDLEFYRSRILEVLE  2050
2051  DDQYKVILIDYGNTTVVDKLYELPQEFTLIKPVAEICSMEPSAIFEKNKA  2100
2101  LTLTTFDALLDSCKGVVAVEFVNKSASPPVVRLTTKDKRSLKIYEHLQKL  2150
2151  VQAELKLIQKRNENSECIISYGNSPKSFYVQMKHNSADLDLIVKTLQSLK  2200
2201  KEKLKKLIDPTTNSNGVCYSQEDACYYRCSIKSVLDPSQGFEVFLLDYGN  2250
2251  TLVVPEVWQLPQEIEPIPSLALHCQLSKIPMDVSDEKLEEAFAALLEQHF  2300
2301  GELYEITTQPNEDETKPLIAELRINYKDFVQELVSTVTGVQKPLEAELHN  2350
2351  CVVVQFDGPMSFYVQMESDVPALEQMTDKLLDAEQDLPAFSDLKEGALCV  2400
2401  AQFPEDEVFYRAQIRKVLDDGKCEVHFIDFGNNAVTQQFRQLPEELAKPA  2450
2451  RYSRHCELDASTISKCDAALLQSFIDTRFSETFQVEILATKGTGTHVVRL  2500
2501  FYQSKNISEKLQECQ                                     2515

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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