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

NucPred

Fetching P08941 from www.uniprot.org...

The NucPred score for your sequence is 0.44 (see score help below)

   1  MRNACLLLNRLGAFYFIWISAAYCSFSKNCQDLCTSNLEGELGIANLCNV    50
  51  SDINVACTQGCQFWNATEQVNCPLKCNKTYTRECETVSCKFGCSRAEDAY   100
 101  GVEAQNCLNKPGAPFASSIGSHNITLGWKPANISEVKYIIQWKFHQLPGD   150
 151  WRYTEVVSETSYTVKDLQAFTEYEFRVVWIITSQLQLHSPPSPSYRTHAS   200
 201  GVPTTAPIIKDIQSSSPNTVEVSWFPPLFPNGLIVGYNLVLTSENHELLR   250
 251  ASRGHSFQFYSTFPNSTYRFSIVAVNEAGAGPPAEANITTPESKVKEKAK   300
 301  WLFLSRNQSLRKRYMEHFLEAAHCLQNGIIHHNITGISVNVYQQVVYFSE   350
 351  GNSIWVKGVVDMSDVSDLTLFYTGWGNITSISVDWLYQRMYFVMNEKIHV   400
 401  CQLENCTAAEDITPPYETSPRKIVADPYNGYIFCLLEDGIYRANLPLFPD   450
 451  TASAASLVVKSHTLRDFMINFQSKRLIFFNKTEQAFVSGFLDGSEFHTLR   500
 501  AHVPLDDMESFVYEDNIFTVTDGRAVFHEEISQVGSSSFNEYVVDCSLEY   550
 551  PEYFGFGNLLFYAASTQPYPLPTLPRLVTVLFGSDQAVISWSPPEYTIGT   600
 601  SRSAWQNWTYDVKVSSQSTFEEEWVVSNITDTRFAVKNLVSFTEYEMSVR   650
 651  AVSPAGEGPWSEPFRGMTFEEAEEEPYILAVGAEGLWKQRLDSYGPGEFL   700
 701  YPHIRNISDLDWYNDTLYWSNSMGKVQTWSMNKKEGTTENSYVPDIKNAR   750
 751  MLAFDWLGQCLYWAGKANTIYRKSLLGDHMDVVAHVVYVVKDLAVDSVNG   800
 801  YLYWATTYTVESARLNGEEYLILQEHLQFSGKQVVGLALDLTSGFLYWLV   850
 851  QDGLCLNLYRISICKESCGNIMVTEISAWSVSEVSQNALQYYSGRLFWIN   900
 901  RLKFITTQELNQSISIPFSEPAEFAAFTLVHTSLKPLPGNFSFTPKVIPS   950
 951  SVPESSFKIKGNSSSFHIIWNASTDVQWGTVFYCVGSNALQMRTLESERC  1000
1001  LHPHDLTVPSYKVDWLEPFTLFDFSVTPYTYWGKAPTTSVYLRAPEGVPS  1050
1051  APANPRIYVLHSNTHEGEEKVLVELRWDKPERDNGVLTQFRVYYQLLYES  1100
1101  GAADTLMEWNVSDVKPTALLFSIRDEHPRLTVRFQVQAFTSVGPGPMSDV  1150
1151  AQRNSSDIFPVPTLITFSSNKLFLTDIDSNHTIWEVLTNRNIKDICYTAD  1200
1201  DDKVYYILEDSLFLLNVQSTSESQLFEDVFLRNVTAITVDWIARHLFVAM  1250
1251  KTSWNETQVFFIDLELKTKSLKALNIQLGKRNSTISSLLSYPFLSRLYWI  1300
1301  EELDYGSRMFYYDILNNTMYHILGYESVEEKMRNYCNCNVAEAELGRPIS  1350
1351  IDVTDIKKPQLLFIRGRDEIWASDVDACHCWRITKIPSFQGTKIGSLTVD  1400
1401  KQFIYWTIEKKEYTEICLADKESTRHSLQRKANHELKILAYSSAMQSYPD  1450
1451  KKCLTPLLDTEKPTILDTTNTSFTLSLPSVTTQQLCPSISQPTPTYLVFF  1500
1501  REITSNHENSTYHFSTLLQKTLEIQEPIAVINNLKPFSTYAIQVAVKNYY  1550
1551  SNQNQLAVGREAISTTLYGVPEGVDSIKTVVLSDTTINISWSEPLEPNGP  1600
1601  LESIRYQISVNLLSLFPEAPLRKSEFPNGTLSWSVSDLQSGTNNLFKVLA  1650
1651  FHPNENWFSESVPVIAKTFETPLSPSNIIPRNTSFQLEWRAPLHINGTSF  1700
1701  WFELSKWQTRSDWFSPASTTCTVGPVYTCNLTGTLPSANYLVRATVVYVT  1750
1751  GMKSTSSPTSFKTTAGVPSKPGTPKRAEDSKNSVQWEKAEDNGSNLTYYI  1800
1801  LESRKQSGNTNKVKSLWVVVYNGSCDNICTWKAENLEGTFQFRAAAANML  1850
1851  GLGEYSDTSKDIVLAKDTVTSPDITAIVAVIGAVVLGLTIIILFGFVWHQ  1900
1901  RWKSRKPASTGQIVLVKEDKELAQLRGMAETVGLANACYAVSTLPSQAEI  1950
1951  ESLPAFPRDKLNLHKLLGSGAFGEVYEGTALDILADGSGESRVAVKTLKR  2000
2001  GATDQEKSEFLKEAHLMSKFDHPHILKLLGVCLLNEPQYLILELMEGGDL  2050
2051  LSYLRGARKQKFQSPLLTLTDLLDICLDICKGCVYLEKMRFIHRDLAARN  2100
2101  CLVSEKQYGSCSRVVKIGDFGLARDIYKNDYYRKRGEGLINVRWMAPESL  2150
2151  IDGVFTNHSDVWAFGVLVWETLTLGQQPYPGLSNIEVLHHVRSGGRLESP  2200
2201  NNCPDDIRDLMTRCWAQDPHNRPTFFYIQHKLQEIRHSPLCFSYFLGDKE  2250
2251  SVAGFINQAFEDIDVPPADSDSILSTTLMEARDQEGLNYLVVVKESNQDQ  2300
2301  GSISSAELTSV                                         2311

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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