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

NucPred

Fetching Q85WV5 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MKKKKGERGGSKEMKKRRSWIIKLEEIQSYQFLCNPWTKSNLMRFLIQIL    50
  51  SHRERLIKLFDPRILSTLLLRDLRRSNPYFLVKGIVVLTLSILIYHFNHK   100
 101  SSMIEKKNFYSMKLFPIHNFMELGNETPEEYLKPFTKNWLIFPHLFLSFQ   150
 151  LKRSYNRFIEHFDPISFNSGYGRNTNKKDEMISENQGPPSKTHLENNEKD   200
 201  LNLKIDSTLNSTENEYWEPEKDLCEDSFIEREQTKIEIESDLSSKCLSEY   250
 251  YPISWAKELFTEDQRYTEENSFPLERKRFIENFTKSIRYSFFYIWPMDEP   300
 301  CMGGPSATKKPIEDFNLSKRLLKRQQNVFSQYLRDSKSYSLMNRIVDLWK   350
 351  IKTYFEIENSSSNYAIPSDPGWNILNILHNNFRSKTKKIVLEMTDQFTLS   400
 401  ITKPSQVHDQIYCNIYYYMNPLYELNKNGSLRSDRIFNHREKLKNQSLWV   450
 451  LLNIIDKADDYLDQIIDKQLSQIDSKNRLEIGTPFNNYRTEALSWYESIR   500
 501  YKIARYSENLFNRFYFINRFSHNLKNQIRTNWIENENLNNVTKDTIDRHS   550
 551  SSWKKIQREWLNRSIIRTDKNINRNLNVYKWSHQTEYFMKYLKHKKNYFQ   600
 601  RVFDLIESCTNTNRNKIGWKDYFQFFQHTVKILNSNFDIISNLNSKFDIV   650
 651  ISILDSHLNKLKSIDPQLLKKNNLDINDLLDLMGTLIVHLKKLKPFLFLL   700
 701  DDHNLSQRSKLLIDEGTIAPFVPNDIPINPSIIDFFYNEKNRMESFDNTD   750
 751  FSTISNDRENWLNPVKLSDQSSLRASFHGANTLQFFDYLHHPRPNYRKRL   800
 801  PSDMKRIYIKRKNLTYGQLFNLLLIHNNISSLLIGEIGPVHSEKETISLI   850
 851  KSQVSNIFLPKYLQRKRSGEQPFVLIYDLYRSFNLLTQLNPFVRDKRYIS   900
 901  SIEEISTTPLTKEQIVNLEKTFCQPFFNRSDSEENNLDKCLKRGFSSNVG   950
 951  LIQTRSYQDDLLSEIFSNKNQEMFHRIQDWFVTKSFKNIIGNEGIDGRST  1000
1001  LSNSSKEEQKIKPSPHFNEPAKKQEMYRISQIDSILSKWDLFKTYMPWFF  1050
1051  TSAWCKYLENMLLYTLPEILLHGSNPFVSILQDIKHNIMLKWNILWELSH  1100
1101  PLWEPIKWKLRTNLTNLLNFRFRTTLMNKFFSSCEDCFIEETSDREWTHL  1150
1151  RLLNARRYEYGILIPFFVLTYSILRYFKVIYSAFINLKIDFELIQYLEDP  1200
1201  SYVIELQKLINPPVYNYLLYYIDIESLPSTKRKRKNRKLNLLITIIRELN  1250
1251  GLCSSMDISEKEMEILVQFLMTEKNLSQFESNMTVSHIFLKKEFGDQITG  1300
1301  QPGLIHLRYLAHTYQKGLMNYELNPFCLAENRIFLAFYQKITSSQILCQP  1350
1351  NPKMPFSFHSGSLFSKGILLIGPMGTGRSYLIKSLAADSYVPLIRISLKK  1400
1401  LLYGKFLYYPDPGRIPTEFNTFWRDTIDHFHITFELAKRMSPCIIWIPNI  1450
1451  HELNVNDTITHLFGLGFTDSFLGLLLNYISRGGEKDSIRNILFIASTHIP  1500
1501  QRVDPALIAPNRLDSSINIRMLVIPQRQREFPILLCSKGLYSEKEVSCPD  1550
1551  EFGSITIDSDARDLAALANEALITSITRKKSVIDTNTIRYAIYSQICHLQ  1600
1601  SMDNQVGSSQNDERLIYKVGKAFIQNTLRRNSPMNPLSTKKELWKKRFCY  1650
1651  LSEWYLEPSIAETTMKELTILPHILGCLAGSAARDSWSISERNRENWIPL  1700
1701  DKFAEHDLDLASSLLESILVEFPFSRLGICRGKSDKDQSKFDKDQITFVP  1750
1751  QPKMRNNHMIRFLKEYELKFTIATKKMYRDMDMDEELIKSVVWTPRTWRL  1800
1801  SFLRSNRFDHTKTPNSLGSSYRFGSKKKAQIERSKFARQYPRQYKSSEKP  1850
1851  TFCRGKRFLWDPFLFQEQRPVFSRREFFADEELLKRLYITYGSRRLLAKP  1900
1901  NFFPKQSFQSAFHRYDSKYGINPGLIMNSWKPLSLRHRHIEHFKHIQEIG  1950
1951  IHLERIQPYSSPYLYKCWLIENSRERVDRFQSLIHRQKRWLGTNSLLSNE  2000
2001  SFLYNTLFESYQYLSNLFLSNRVLLDQITKTLLEKECLFPNEIEHSIYTT  2050
2051  GLRFDISWENLE                                        2062

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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