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

NucPred

Fetching O00763 from www.uniprot.org...

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

   1  MVLLLCLSCLIFSCLTFSWLKIWGKMTDSKPITKSKSEANLIPSQEPFPA    50
  51  SDNSGETPQRNGEGHTLPKTPSQAEPASHKGPKDAGRRRNSLPPSHQKPP   100
 101  RNPLSSSDAAPSPELQANGTGTQGLEATDTNGLSSSARPQGQQAGSPSKE   150
 151  DKKQANIKRQLMTNFILGSFDDYSSDEDSVAGSSRESTRKGSRASLGALS   200
 201  LEAYLTTGEAETRVPTMRPSMSGLHLVKRGREHKKLDLHRDFTVASPAEF   250
 251  VTRFGGDRVIEKVLIANNGIAAVKCMRSIRRWAYEMFRNERAIRFVVMVT   300
 301  PEDLKANAEYIKMADHYVPVPGGPNNNNYANVELIVDIAKRIPVQAVWAG   350
 351  WGHASENPKLPELLCKNGVAFLGPPSEAMWALGDKIASTVVAQTLQVPTL   400
 401  PWSGSGLTVEWTEDDLQQGKRISVPEDVYDKGCVKDVDEGLEAAERIGFP   450
 451  LMIKASEGGGGKGIRKAESAEDFPILFRQVQSEIPGSPIFLMKLAQHARH   500
 501  LEVQILADQYGNAVSLFGRDCSIQRRHQKIVEEAPATIAPLAIFEFMEQC   550
 551  AIRLAKTVGYVSAGTVEYLYSQDGSFHFLELNPRLQVEHPCTEMIADVNL   600
 601  PAAQLQIAMGVPLHRLKDIRLLYGESPWGVTPISFETPSNPPLARGHVIA   650
 651  ARITSENPDEGFKPSSGTVQELNFRSSKNVWGYFSVAATGGLHEFADSQF   700
 701  GHCFSWGENREEAISNMVVALKELSIRGDFRTTVEYLINLLETESFQNND   750
 751  IDTGWLDYLIAEKVQAEKPDIMLGVVCGALNVADAMFRTCMTDFLHSLER   800
 801  GQVLPADSLLNLVDVELIYGGVKYILKVARQSLTMFVLIMNGCHIEIDAH   850
 851  RLNDGGLLLSYNGNSYTTYMKEEVDSYRITIGNKTCVFEKENDPTVLRSP   900
 901  SAGKLTQYTVEDGGHVEAGSSYAEMEVMKMIMTLNVQERGRVKYIKRPGA   950
 951  VLEAGCVVARLELDDPSKVHPAEPFTGELPAQQTLPILGEKLHQVFHSVL  1000
1001  ENLTNVMSGFCLPEPVFSIKLKEWVQKLMMTLRHPSLPLLELQEIMTSVA  1050
1051  GRIPAPVEKSVRRVMAQYASNITSVLCQFPSQQIATILDCHAATLQRKAD  1100
1101  REVFFINTQSIVQLVQRYRSGIRGYMKTVVLDLLRRYLRVEHHFQQAHYD  1150
1151  KCVINLREQFKPDMSQVLDCIFSHAQVAKKNQLVIMLIDELCGPDPSLSD  1200
1201  ELISILNELTQLSKSEHCKVALRARQILIASHLPSYELRHNQVESIFLSA  1250
1251  IDMYGHQFCPENLKKLILSETTIFDVLPTFFYHANKVVCMASLEVYVRRG  1300
1301  YIAYELNSLQHRQLPDGTCVVEFQFMLPSSHPNRMTVPISITNPDLLRHS  1350
1351  TELFMDSGFSPLCQRMGAMVAFRRFEDFTRNFDEVISCFANVPKDTPLFS  1400
1401  EARTSLYSEDDCKSLREEPIHILNVSIQCADHLEDEALVPILRTFVQSKK  1450
1451  NILVDYGLRRITFLIAQEKEFPKFFTFRARDEFAEDRIYRHLEPALAFQL  1500
1501  ELNRMRNFDLTAVPCANHKMHLYLGAAKVKEGVEVTDHRFFIRAIIRHSD  1550
1551  LITKEASFEYLQNEGERLLLEAMDELEVAFNNTSVRTDCNHIFLNFVPTV  1600
1601  IMDPFKIEESVRYMVMRYGSRLWKLRVLQAEVKINIRQTTTGSAVPIRLF  1650
1651  ITNESGYYLDISLYKEVTDSRSGNIMFHSFGNKQGPQHGMLINTPYVTKD  1700
1701  LLQAKRFQAQTLGTTYIYDFPEMFRQALFKLWGSPDKYPKDILTYTELVL  1750
1751  DSQGQLVEMNRLPGGNEVGMVAFKMRFKTQEYPEGRDVIVIGNDITFRIG  1800
1801  SFGPGEDLLYLRASEMARAEGIPKIYVAANSGARIGMAEEIKHMFHVAWV  1850
1851  DPEDPHKGFKYLYLTPQDYTRISSLNSVHCKHIEEGGESRYMITDIIGKD  1900
1901  DGLGVENLRGSGMIAGESSLAYEEIVTISLVTCRAIGIGAYLVRLGQRVI  1950
1951  QVENSHIILTGASALNKVLGREVYTSNNQLGGVQIMHYNGVSHITVPDDF  2000
2001  EGVYTILEWLSYMPKDNHSPVPIITPTDPIDREIEFLPSRAPYDPRWMLA  2050
2051  GRPHPTLKGTWQSGFFDHGSFKEIMAPWAQTVVTGRARLGGIPVGVIAVE  2100
2101  TRTVEVAVPADPANLDSEAKIIQQAGQVWFPDSAYKTAQAVKDFNREKLP  2150
2151  LMIFANWRGFSGGMKDMYDQVLKFGAYIVDGLRQYKQPILIYIPPYAELR  2200
2201  GGSWVVIDATINPLCIEMYADKESRGGVLEPEGTVEIKFRKKDLIKSMRR  2250
2251  IDPAYKKLMEQLGEPDLSDKDRKDLEGRLKAREDLLLPIYHQVAVQFADF  2300
2301  HDTPGRMLEKGVISDILEWKTARTFLYWRLRRLLLEDQVKQEILQASGEL  2350
2351  SHVHIQSMLRRWFVETEGAVKAYLWDNNQVVVQWLEQHWQAGDGPRSTIR  2400
2401  ENITYLKHDSVLKTIRGLVEENPEVAVDCVIYLSQHISPAERAQVVHLLS  2450
2451  TMDSPAST                                            2458

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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