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

NucPred

Fetching Q6FX42 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MESQIRYIDELIAGFNGSCKIERVNEGNCAAQSSNTEERKLIQAVQALLR    50
  51  ILNDLNHNSADLIFQKCLGGLDRILHHNPYIMALSISSEDSGNLMIMDLI   100
 101  DKMLGLTERCSYNIHRMWYIRRNIIRWITSSTRLFGSDFKRIINLKIKKI   150
 151  LNELETKCKLFLFTHQNVEPQEFISTLTLLHTILYWISADSNKLGDYFYW   200
 201  IQGSSSLNEWDLHFQKYIRIAMYLFTSFQIKIDANSSYFEKFNLLQANFI   250
 251  MLVANYQTSRTLSGGFNSIAISIQHLKFTLEVISEFMRNRSFLSKNETLI   300
 301  TKSLLKIYYLSVCKASSNKNDILSIFLDYIPVVECINSKHQFNENYDSEL   350
 351  ERSLLLLYFDMKRRYADPDELQFIDSFDIWSHPDCIDEVSIITQPIKKNS   400
 401  KQIEKLQRSILKSYTVNIKQIHSFLFKELNSLEPGILDRNGDHYKAVVKE   450
 451  ISISIKRSLKIRDSKKIITWLRVLSRMACIEDKLINTKQNISEFFHTTND   500
 501  FCNYCDSIHDGNFLNNIEPSRPLAQDQSEIFSMINKYFILNPDLKKFSMS   550
 551  IKCGLFIVIERIFAHFQPTALMNENNQIAPLFSFIEDSFIDSDRHVRLLI   600
 601  CKILPLWNTSNHNNSEDEMSMHLIQFLQKVNSPLLLETVVLSWSKITLTT   650
 651  HGDVFDTLLLKLIDLFNSNNFTLHIMMKEQLIRMSSLLNKTPYQLLSPVL   700
 701  PIILRQLSKNLNEKKLSFQRLCDLVGYTGKVILDIFQKYVIPYATVQYKS   750
 751  DVFSEVAKIMCDDDTSMLLQQKHNLLTKNSRQIFAVALVKHGFFSLDTME   800
 801  TLFLNRVPSYDRRYIGAYLPDYKTLAEVTKLYKNNEITDSSDIENENMVL   850
 851  CSLRYLITNFESDKRHGTEYKDINKWSDKKENQFQNNLQDNILGIFQVFS   900
 901  SDMHDVEGKTTYYEKLRVINGISFLVKHASNKCIISALAQLSICLQSGLE   950
 951  IPEVRYLSMRCWFLLIQRLNEEELTTVIDAPVAFILRKWPTFNKKLQLKA  1000
1001  LEVLTALIRTKNSLLMKMKPYISISLLSNESIPILDIDTNFSRQAARLRN  1050
1051  TIDLVPIFVKNLQSNNKFVIEQNLDDIKFHLKRRQGELLQYDKYGNLQLN  1100
1101  AVPSLIGALLEVAHKYRTIDHEICKKCAKCISMVGVPDIRRIDLRGDRKE  1150
1151  KWKVFDFNDYSKTTEFLIWLIDDILVPSFWQSENPNKQLFFALVMQESLK  1200
1201  YCGLSSQSWDINEPDKFPEQLELWNKFNSISKTTLYPLLSSLYLAQSWKE  1250
1251  YVPIKYPSLNFRDGYKTWIKNFTLDLLKTGTTEDHPLHVFSSLIREDDGS  1300
1301  LSSFLLPYIAQDIIIKAQSGTEYESLMDNILIELQSVVTYEIDGLNHLQR  1350
1351  DSLKMCYEAVFSILEYCKKWATMFRQDYNNANGTFLIKEDKYLKMLKRID  1400
1401  YFINSIPLDLLANKSLETNAFERSALYLEECYRHSDIHDRNLNSTLKSLQ  1450
1451  MTYEEIGDIDSIDGLLKSFASTSFETKIEELQYSNKWQMALECFDILADI  1500
1501  TKHDSTAQIMTKSMFDHHLYKNVIQTVPKLVPDNIQKLNESNTNLLIRAL  1550
1551  ESSILEGDLKSIEKWSSKIELMTTINDPELTLQYNLGKALLSISKGNHIK  1600
1601  AGQFLDNCYQITGIQYTSTSNSTTLLKTQSLLTKLHGLHDLNMLNFSKDD  1650
1651  FELQSNMQLLDLRRGKVGPDFDPNYYILSIRKTFDKIHKNPITKTDLVDT  1700
1701  YFAIAQEARVNSRLDIASKALIFCLEKGHPYSELEFAEILWKDGENDRAL  1750
1751  KLVREINQKNEKSSSVSVRNKAEVLLKYTEWLDISNNSASEQIITQYKNI  1800
1801  FALEPEWEQPYYSIGLYFSRLLERRKAEGYVSDGKLEFKSISYFLLAFEK  1850
1851  NTVKVRENLPKVITFWLDTAAAVITETSPNRNTILKKVTTDICKQIETAI  1900
1901  RNCPTYIWYSVLTQLLSRLLHPHLSSAKLIMHILLSLAVEYPSHILWHIS  1950
1951  VLCQSNSSKRVKCGQDILEKFRAHSDNQEDIINSSIYLTSSLTRICLQEV  2000
2001  KSSSSRSGRSLVSDFKFDVNIAPTPMTVPVRKNLEMISPLSAETMKSYQP  2050
2051  FRPTVSIAKFASSYKIFSSLKKPKKITIIGSDGMLYEIMCKKEDVRQDNQ  2100
2101  YMQFAATMDFLLSKDLDSSKRDLGITVYSVLSLREDCGLLEIVPDVVTLR  2150
2151  SIFTTKYESKKIKYSMKALYEKWQGLADELKPVFFNEQTKKFSPVLHEWF  2200
2201  LENFPDPINWYRARNLYSRSYAVMAMVGYILGLGDRHCENILLDIKTGKV  2250
2251  LHVDFDCLFEKGENLPVPEIVPFRLTQNLQDALGILGTEGTFKKSSEVTL  2300
2301  SLMRQNEVALMNIIETIMYDRNMDHSIQKALRKLRNKIRGIDPRDGLLLS  2350
2351  VSGQAETLIQEATSTENLSKMYIGWLPFW                       2379

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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