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

NucPred

Fetching P12263 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MQLELSTCVFLCLLPLGFSAIRRYYLGAVELSWDYRQSELLRELHVDTRF    50
  51  PATAPGALPLGPSVLYKKTVFVEFTDQLFSVARPRPPWMGLLGPTIQAEV   100
 101  YDTVVVTLKNMASHPVSLHAVGVSFWKSSEGAEYEDHTSQREKEDDKVLP   150
 151  GKSQTYVWQVLKENGPTASDPPCLTYSYLSHVDLVKDLNSGLIGALLVCR   200
 201  EGSLTRERTQNLHEFVLLFAVFDEGKSWHSARNDSWTRAMDPAPARAQPA   250
 251  MHTVNGYVNRSLPGLIGCHKKSVYWHVIGMGTSPEVHSIFLEGHTFLVRH   300
 301  HRQASLEISPLTFLTAQTFLMDLGQFLLFCHISSHHHGGMEAHVRVESCA   350
 351  EEPQLRRKADEEEDYDDNLYDSDMDVVRLDGDDVSPFIQIRSVAKKHPKT   400
 401  WVHYISAEEEDWDYAPAVPSPSDRSYKSLYLNSGPQRIGRKYKKARFVAY   450
 451  TDVTFKTRKAIPYESGILGPLLYGEVGDTLLIIFKNKASRPYNIYPHGIT   500
 501  DVSALHPGRLLKGWKHLKDMPILPGETFKYKWTVTVEDGPTKSDPRCLTR   550
 551  YYSSSINLEKDLASGLIGPLLICYKESVDQRGNQMMSDKRNVILFSVFDE   600
 601  NQSWYLAENIQRFLPNPDGLQPQDPEFQASNIMHSINGYVFDSLQLSVCL   650
 651  HEVAYWYILSVGAQTDFLSVFFSGYTFKHKMVYEDTLTLFPFSGETVFMS   700
 701  MENPGLWVLGCHNSDLRNRGMTALLKVYSCDRDIGDYYDNTYEDIPGFLL   750
 751  SGKNVIEPRSFAQNSRPPSASQKQFQTITSPEDDVELDPQSGERTQALEE   800
 801  LSVPSGDGSMLLGQNPAPHGSSSSDLQEARNEADDYLPGARERNTAPSAA   850
 851  ARLRPELHHSAERVLTPEPEKELKKLDSKMSSSSDLLKTSPTIPSDTLSA   900
 901  ETERTHSLGPPHPQVNFRSQLGAIVLGKNSSHFIGAGVPLGSTEEDHESS   950
 951  LGENVSPVESDGIFEKERAHGPASLTKDDVLFKVNISLVKTNKARVYLKT  1000
1001  NRKIHIDDAALLTENRASATFMDKNTTASGLNHVSNWIKGPLGKNPLSSE  1050
1051  RGPSPELLTSSGSGKSVKGQSSGQGRIRVAVEEEELSKGKEMMLPNSELT  1100
1101  FLTNSADVQGNDTHSQGKKSREEMERREKLVQEKVDLPQVYTATGTKNFL  1150
1151  RNIFHQSTEPSVEGFDGGSHAPVPQDSRSLNDSAERAETHIAHFSAIREE  1200
1201  APLEAPGNRTGPGPRSAVPRRVKQSLKQIRLPLEEIKPERGVVLNATSTR  1250
1251  WSESSPILQGAKRNNLSLPFLTLEMAGGQGKISALGKSAAGPLASGKLEK  1300
1301  AVLSSAGLSEASGKAEFLPKVRVHREDLLPQKTSNVSCAHGDLGQEIFLQ  1350
1351  KTRGPVNLNKVNRPGRTPSKLLGPPMPKEWESLEKSPKSTALRTKDIISL  1400
1401  PLDRHESNHSIAAKNEGQAETQREAAWTKQGGPGRLCAPKPPVLRRHQRD  1450
1451  ISLPTFQPEEDKMDYDDIFSTETKGEDFDIYGEDENQDPRSFQKRTRHYF  1500
1501  IAAVEQLWDYGMSESPRALRNRAQNGEVPRFKKVVFREFADGSFTQPSYR  1550
1551  GELNKHLGLLGPYIRAEVEDNIMVTFKNQASRPYSFYSSLISYPDDQEQG  1600
1601  AEPRHNFVQPNETRTYFWKVQHHMAPTEDEFDCKAWAYFSDVDLEKDVHS  1650
1651  GLIGPLLICRANTLNAAHGRQVTVQEFALFFTIFDETKSWYFTENVERNC  1700
1701  RAPCHLQMEDPTLKENYRFHAINGYVMDTLPGLVMAQNQRIRWYLLSMGS  1750
1751  NENIHSIHFSGHVFSVRKKEEYKMAVYNLYPGVFETVEMLPSKVGIWRIE  1800
1801  CLIGEHLQAGMSTTFLVYSKECQAPLGMASGRIRDFQITASGQYGQWAPK  1850
1851  LARLHYSGSINAWSTKDPHSWIKVDLLAPMIIHGIMTQGARQKFSSLYIS  1900
1901  QFIIMYSLDGRNWQSYRGNSTGTLMVFFGNVDASGIKHNIFNPPIVARYI  1950
1951  RLHPTHYSIRSTLRMELMGCDLNSCSMPLGMQNKAISDSQITASSHLSNI  2000
2001  FATWSPSQARLHLQGRTNAWRPRVSSAEEWLQVDLQKTVKVTGITTQGVK  2050
2051  SLLSSMYVKEFLVSSSQDGRRWTLFLQDGHTKVFQGNQDSSTPVVNALDP  2100
2101  PLFTRYLRIHPTSWAQHIALRLEVLGCEAQDLY                   2133

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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