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

NucPred

Fetching Q9HD67 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MDNFFTEGTRVWLRENGQHFPSTVNSCAEGIVVFRTDYGQVFTYKQSTIT    50
  51  HQKVTAMHPTNEEGVDDMASLTELHGGSIMYNLFQRYKRNQIYTYIGSIL   100
 101  ASVNPYQPIAGLYEPATMEQYSRRHLGELPPHIFAIANECYRCLWKRHDN   150
 151  QCILISGESGAGKTESTKLILKFLSVISQQSLELSLKEKTSCVERAILES   200
 201  SPIMEAFGNAKTVYNNNSSRFGKFVQLNICQKGNIQGGRIVDYLLEKNRV   250
 251  VRQNPGERNYHIFYALLAGLEHEEREEFYLSTPENYHYLNQSGCVEDKTI   300
 301  SDQESFREVITAMDVMQFSKEEVREVSRLLAGILHLGNIEFITAGGAQVS   350
 351  FKTALGRSAELLGLDPTQLTDALTQRSMFLRGEEILTPLNVQQAVDSRDS   400
 401  LAMALYACCFEWVIKKINSRIKGNEDFKSIGILDIFGFENFEVNHFEQFN   450
 451  INYANEKLQEYFNKHIFSLEQLEYSREGLVWEDIDWIDNGECLDLIEKKL   500
 501  GLLALINEESHFPQATDSTLLEKLHSQHANNHFYVKPRVAVNNFGVKHYA   550
 551  GEVQYDVRGILEKNRDTFRDDLLNLLRESRFDFIYDLFEHVSSRNNQDTL   600
 601  KCGSKHRRPTVSSQFKDSLHSLMATLSSSNPFFVRCIKPNMQKMPDQFDQ   650
 651  AVVLNQLRYSGMLETVRIRKAGYAVRRPFQDFYKRYKVLMRNLALPEDVR   700
 701  GKCTSLLQLYDASNSEWQLGKTKVFLRESLEQKLEKRREEEVSHAAMVIR   750
 751  AHVLGFLARKQYRKVLYCVVIIQKNYRAFLLRRRFLHLKKAAIVFQKQLR   800
 801  GQIARRVYRQLLAEKREQEEKKKQEEEEKKKREEEERERERERREAELRA   850
 851  QQEEETRKQQELEALQKSQKEAELTRELEKQKENKQVEEILRLEKEIEDL   900
 901  QRMKEQQELSLTEASLQKLQERRDQELRRLEEEACRAAQEFLESLNFDEI   950
 951  DECVRNIERSLSVGSEFSSELAESACEEKPNFNFSQPYPEEEVDEGFEAD  1000
1001  DDAFKDSPNPSEHGHSDQRTSGIRTSDDSSEEDPYMNDTVVPTSPSADST  1050
1051  VLLAPSVQDSGSLHNSSSGESTYCMPQNAGDLPSPDGDYDYDQDDYEDGA  1100
1101  ITSGSSVTFSNSYGSQWSPDYRCSVGTYNSSGAYRFSSEGAQSSFEDSEE  1150
1151  DFDSRFDTDDELSYRRDSVYSCVTLPYFHSFLYMKGGLMNSWKRRWCVLK  1200
1201  DETFLWFRSKQEALKQGWLHKKGGGSSTLSRRNWKKRWFVLRQSKLMYFE  1250
1251  NDSEEKLKGTVEVRTAKEIIDNTTKENGIDIIMADRTFHLIAESPEDASQ  1300
1301  WFSVLSQVHASTDQEIQEMHDEQANPQNAVGTLDVGLIDSVCASDSPDRP  1350
1351  NSFVIITANRVLHCNADTPEEMHHWITLLQRSKGDTRVEGQEFIVRGWLH  1400
1401  KEVKNSPKMSSLKLKKRWFVLTHNSLDYYKSSEKNALKLGTLVLNSLCSV  1450
1451  VPPDEKIFKETGYWNVTVYGRKHCYRLYTKLLNEATRWSSAIQNVTDTKA  1500
1501  PIDTPTQQLIQDIKENCLNSDVVEQIYKRNPILRYTHHPLHSPLLPLPYG  1550
1551  DINLNLLKDKGYTTLQDEAIKIFNSLQQLESMSDPIPIIQGILQTGHDLR  1600
1601  PLRDELYCQLIKQTNKVPHPGSVGNLYSWQILTCLSCTFLPSRGILKYLK  1650
1651  FHLKRIREQFPGSEMEKYALFTYESLKKTKCREFVPSRDEIEALIHRQEM  1700
1701  TSTVYCHGGGSCKITINSHTTAGEVVEKLIRGLAMEDSRNMFALFEYNGH  1750
1751  VDKAIESRTVVADVLAKFEKLAATSEVGDLPWKFYFKLYCFLDTDNVPKD  1800
1801  SVEFAFMFEQAHEAVIHGHHPAPEENLQVLAALRLQYLQGDYTLHAAIPP  1850
1851  LEEVYSLQRLKARISQSTKTFTPCERLEKRRTSFLEGTLRRSFRTGSVVR  1900
1901  QKVEEEQMLDMWIKEEVSSARASIIDKWRKFQGMNQEQAMAKYMALIKEW  1950
1951  PGYGSTLFDVECKEGGFPQELWLGVSADAVSVYKRGEGRPLEVFQYEHIL  2000
2001  SFGAPLANTYKIVVDERELLFETSEVVDVAKLMKAYISMIVKKRYSTTRS  2050
2051  ASSQGSSR                                            2058

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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