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

NucPred

Fetching Q00955 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MSEESLFESSPQKMEYEITNYSERHTELPGHFIGLNTVDKLEESPLRDFV    50
  51  KSHGGHTVISKILIANNGIAAVKEIRSVRKWAYETFGDDRTVQFVAMATP   100
 101  EDLEANAEYIRMADQYIEVPGGTNNNNYANVDLIVDIAERADVDAVWAGW   150
 151  GHASENPLLPEKLSQSKRKVIFIGPPGNAMRSLGDKISSTIVAQSAKVPC   200
 201  IPWSGTGVDTVHVDEKTGLVSVDDDIYQKGCCTSPEDGLQKAKRIGFPVM   250
 251  IKASEGGGGKGIRQVEREEDFIALYHQAANEIPGSPIFIMKLAGRARHLE   300
 301  VQLLADQYGTNISLFGRDCSVQRRHQKIIEEAPVTIAKAETFHEMEKAAV   350
 351  RLGKLVGYVSAGTVEYLYSHDDGKFYFLELNPRLQVEHPTTEMVSGVNLP   400
 401  AAQLQIAMGIPMHRISDIRTLYGMNPHSASEIDFEFKTQDATKKQRRPIP   450
 451  KGHCTACRITSEDPNDGFKPSGGTLHELNFRSSSNVWGYFSVGNNGNIHS   500
 501  FSDSQFGHIFAFGENRQASRKHMVVALKELSIRGDFRTTVEYLIKLLETE   550
 551  DFEDNTITTGWLDDLITHKMTAEKPDPTLAVICGAATKAFLASEEARHKY   600
 601  IESLQKGQVLSKDLLQTMFPVDFIHEGKRYKFTVAKSGNDRYTLFINGSK   650
 651  CDIILRQLSDGGLLIAIGGKSHTIYWKEEVAATRLSVDSMTTLLEVENDP   700
 701  TQLRTPSPGKLVKFLVENGEHIIKGQPYAEIEVMKMQMPLVSQENGIVQL   750
 751  LKQPGSTIVAGDIMAIMTLDDPSKVKHALPFEGMLPDFGSPVIEGTKPAY   800
 801  KFKSLVSTLENILKGYDNQVIMNASLQQLIEVLRNPKLPYSEWKLHISAL   850
 851  HSRLPAKLDEQMEELVARSLRRGAVFPARQLSKLIDMAVKNPEYNPDKLL   900
 901  GAVVEPLADIAHKYSNGLEAHEHSIFVHFLEEYYEVEKLFNGPNVREENI   950
 951  ILKLRDENPKDLDKVALTVLSHSKVSAKNNLILAILKHYQPLCKLSSKVS  1000
1001  AIFSTPLQHIVELESKATAKVALQAREILIQGALPSVKERTEQIEHILKS  1050
1051  SVVKVAYGSSNPKRSEPDLNILKDLIDSNYVVFDVLLQFLTHQDPVVTAA  1100
1101  AAQVYIRRAYRAYTIGDIRVHEGVTVPIVEWKFQLPSAAFSTFPTVKSKM  1150
1151  GMNRAVSVSDLSYVANSQSSPLREGILMAVDHLDDVDEILSQSLEVIPRH  1200
1201  QSSSNGPAPDRSGSSASLSNVANVCVASTEGFESEEEILVRLREILDLNK  1250
1251  QELINASIRRITFMFGFKDGSYPKYYTFNGPNYNENETIRHIEPALAFQL  1300
1301  ELGRLSNFNIKPIFTDNRNIHVYEAVSKTSPLDKRFFTRGIIRTGHIRDD  1350
1351  ISIQEYLTSEANRLMSDILDNLEVTDTSNSDLNHIFINFIAVFDISPEDV  1400
1401  EAAFGGFLERFGKRLLRLRVSSAEIRIIIKDPQTGAPVPLRALINNVSGY  1450
1451  VIKTEMYTEVKNAKGEWVFKSLGKPGSMHLRPIATPYPVKEWLQPKRYKA  1500
1501  HLMGTTYVYDFPELFRQASSSQWKNFSADVKLTDDFFISNELIEDENGEL  1550
1551  TEVEREPGANAIGMVAFKITVKTPEYPRGRQFVVVANDITFKIGSFGPQE  1600
1601  DEFFNKVTEYARKRGIPRIYLAANSGARIGMAEEIVPLFQVAWNDAANPD  1650
1651  KGFQYLYLTSEGMETLKKFDKENSVLTERTVINGEERFVIKTIIGSEDGL  1700
1701  GVECLRGSGLIAGATSRAYHDIFTITLVTCRSVGIGAYLVRLGQRAIQVE  1750
1751  GQPIILTGAPAINKMLGREVYTSNLQLGGTQIMYNNGVSHLTAVDDLAGV  1800
1801  EKIVEWMSYVPAKRNMPVPILETKDTWDRPVDFTPTNDETYDVRWMIEGR  1850
1851  ETESGFEYGLFDKGSFFETLSGWAKGVVVGRARLGGIPLGVIGVETRTVE  1900
1901  NLIPADPANPNSAETLIQEPGQVWHPNSAFKTAQAINDFNNGEQLPMMIL  1950
1951  ANWRGFSGGQRDMFNEVLKYGSFIVDALVDYKQPIIIYIPPTGELRGGSW  2000
2001  VVVDPTINADQMEMYADVNARAGVLEPQGMVGIKFRREKLLDTMNRLDDK  2050
2051  YRELRSQLSNKSLAPEVHQQISKQLADRERELLPIYGQISLQFADLHDRS  2100
2101  SRMVAKGVISKELEWTEARRFFFWRLRRRLNEEYLIKRLSHQVGEASRLE  2150
2151  KIARIRSWYPASVDHEDDRQVATWIEENYKTLDDKLKGLKLESFAQDLAK  2200
2201  KIRSDHDNAIDGLSEVIKMLSTDDKEKLLKTLK                   2233

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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