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

NucPred

Fetching Q859W7 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MKQKLLENKFSYRKFKLEEIKKYEYLLNSCINWNLIKLVTGIPSNREHLI    50
  51  KLFDLRILSSLILRDLRKSEMKKSLILKSFPLLILSMFIHRMNSRNIVEI   100
 101  NNCHLERIIYGGINYREGRDEISRRYLHSFMKNFSIPLNYPFSTKKGRER   150
 151  YTNNLLRQKKHIWVFKRNLLGKKYIKPVYDKIDFYNFEEWKTLIIKEILP   200
 201  SWKISNQSIDKANILLEDKNIEDLKHFFELYVDDIIRRDYHWKNSLDIIS   250
 251  YRDRKNQVNFNLKNNLEFLDKKLFYCLISAFCEKVLSEVEGPFKHKRIKS   300
 301  TFNLKNIEDFSDFEVTNKEIFKWELHWWKKKIFQFLDKNHESDQSIAKSF   350
 351  TFFQNKRFLFLENYAEFYTWLLYEDSPFHLKKNKQLLDTAKDTFKEDSFQ   400
 401  LNDRRNQIYSFENKGIFLNILHNFSIYVSNKVRKLNHLKIFSDISIKNSY   450
 451  LINKNLVYHGKGSGGTIYEDEKQKTWDTTDFYLKREKYFISKTDFLSRSI   500
 501  EKKCFKSNKYFLDLFLNRGDTNKRSTTESNIHSYDLSSLTKAKRKEVKSG   550
 551  SSYEFLEKDSFFFLMKENFVKDFKSITKDFFSNREKKMTDYFPKLINYAF   600
 601  LDISSIDESNMSFHITGRHLKDFPLNEWRTNIPSRNYMLSDISRMINLSK   650
 651  IRKKFQNVFFVSSISSKRIRQNKNSNDFYLISLIKLNLSWNRPYLCWSTL   700
 701  YKCNKQYIFNRYLKLKERFMRGVEQLNLLITKPNQNYDKILYFQVESEIG   750
 751  KFHKSKENELNYNFFFPLLNGINEDDKFLNEMFHKKVEAHSEENFETYIY   800
 801  PTNHRKKLKLWYELNKGSYICLDNVVKKYYSIYKLKFYLINRMKKLWVER   850
 851  IENGNSSNFIRNIVNGHSSNWKINGREWSDYNIKRDKYINWNSYIYKWFD   900
 901  RTKNLQIFPNWFSDNTSRRWFNEIRFIKPDIFMTYPKKLEKNYYSKVYFI   950
 951  FNTSSNSLLESISKKKNINLRGRVLHNYKKLSRDSEKLIKNKLLPESFLN  1000
1001  KNLIKNIIISLFNNEKNHDIFREFPRKTFSLWIYKNRNNGFNSINNFQKN  1050
1051  LMMNFHNTNTIEFLDYLHDFHFRYDKRLPFFMKEIHIKNYDSTYNKFLRI  1100
1101  LPIYSNLRSLSINKIKPFFFQSRIDITLSIQLQVFNDSLSNYLGRTCNYI  1150
1151  FTSFTNHLYKLLNLLIKINSSIYKETDSCSIQKFLAMTPSGPTILNLKIT  1200
1201  HYDEFFLGELTSNFNGYFEFSSEPNLSHTEIQSYKNELLSEFLIEFRNKN  1250
1251  NRKLQWIKESFLKLNLKENFKYVIGGESIDRISINLDFYEKNKNILPYPS  1300
1301  LSITDFFDKDDKIKVSKKLYFLEKWNFFQNYTSWFFTFEWWRYFSNIPLE  1350
1351  TFPEVLLNITDQSKYISYKTTQYIEEILKDLWKNLNFIFQTNILRKININ  1400
1401  SEIRLLKQINNEQHESIFIYIWSHFQFINLSNAIYLTLISLSVSCFLVSE  1450
1451  NYFSTLIGLDYIDSWRRFKVIEYLRDPLRGSYLVERWIYGNQTQIIRTEN  1500
1501  FFMLLLKNFIHYIKNGRFFLFTRKKLDTWLFHSRTLDLSRRKKDLLVKSV  1550
1551  ITERSLSQYRLNLNLNHNLRNYDFGYKISEKPGFYYLRYLAETYQKDLVN  1600
1601  HSFYSSHLAEKWILLAFWKGMISSQKLWQTKILNHESYRIPIPFELDLFS  1650
1651  SKGILLVGPTEIGKSYLIKNLAADSYVPLIKISISKLLYNKPDVITESWI  1700
1701  NILMESLQRLTLILELAKKMSPCIIWIQDIHELNVNRSTENVESDPTFLL  1750
1751  GILLKYFHTEFISKSTKGIIIIGSTHLPRKVDPALISPNRLDKLMNIRII  1800
1801  DIFERQEKFSILLHSKRFYFKNKLLHFNEFAYRTMGYNGRDLVALANEVS  1850
1851  LINTTQGNSTIYIDAVRLALHRQTLGFTYINNQMLFCQNEGVLLHKIGKA  1900
1901  VIQNIFIKIFPMNPLYIGSDLWKKKFYYLSEWFLEPSVTEPTIKELTLLS  1950
1951  YILGCLAGLAAGDSWSILEHEPENLIPLNKFIENDFDLACGISESFLVEF  2000
2001  SWLEIFQDESINNEIEFFPKIGARHFLNMMQRGISSTTSGKFMYKQDGLR  2050
2051  NRSIFKKTVQYKEKLYELASETTWAPKIWRLSFIRTKSFDWIGRPNDFES  2100
2101  LYSFWFLREKEQTFSVSENSREIFHSSQVAQYKTKEELPYERILSRIRRR  2150
2151  NVEELESQLGFILSEDQFKILGFPELSTQYRIEYELFQKPMLFMGGRFIW  2200
2201  DPTSLSFETRYSVFSRRELFIDEEMRRRLYVTYGARRERERSRSSQKIKQ  2250
2251  FFLRCGYGRDFMNNSSIGWWNGLFLTEKYNIEIFKRIEEISVQLKHPEVF  2300
2301  TPVYLYQSWLIENSREKLSRFDLLNHRERWIKLNNKSFHYFSIHSTLLES  2350
2351  YNYLLNFFISNRILLDEMTKMLLKDGWLFQNEIEHFICKMKK          2392

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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