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

NucPred

Fetching Q00416 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MNSNNPDNNNSNNINNNNKDKDIAPNSDVQLATVYTKAKSYIPQIEQVYQ    50
  51  GTNPNIQEAKLLGELLQVLAEVPKGTHLFCDPILEPISIFSLTIFSFNEE   100
 101  ATATWLKNHFNPILSVCDKCILNFARGKCKMLQHFAIQRHVPHEHVAKFN   150
 151  DIVCQWRVEAVFPILRNISVNDNTGINITNEIETAMYECLCNPHMLRLNK   200
 201  QLKATFEAIFKFFYDTKHRLLDVTNPLSIKTFISGVIFCWCEGSKEENEW   250
 251  SRAFLKDLYSRNFHINLSNLTPDIIEEVYIHILFLQNPANWTEIVVSQFW   300
 301  SRLLPVFNLFDKDVFIEYFQVPKNVESLKKTFKFPLEPIFKMWYNHLSKS   350
 351  YHDKPLDFLLRGLTMFLNKFGSEFWSKIEPFTFHSILDIIFNRDSFPIKL   400
 401  IKIQDNPIVEHQTEVYFQLTGSVTDLLSWTLPFYHALSPSKRIQMVRKVS   450
 451  MAFLRIIANYPSLKSIPKACLMNSATALLRAVLTIKENERAMLYKNDEFE   500
 501  TVLLTKTDSRALLNNPLIQDIIIRSASNPNDFYPGLGAASASVATSTMMV   550
 551  LAECIDFDILLLCHRTFKLYSGKPISEIPISTNVLENVTNKIDLRSFHDG   600
 601  PLLAKQLLVSLKNINGLLIVPSNTAVAEAHNALNQKFLLLSTRLMEKFAD   650
 651  ILPGQLSKILADEDASQGFWSCIFSSDKHLYQAATNILYNTFDVEGRLEG   700
 701  ILAILNSNLTVNLKNINVMLQRLINCEFYEPCPRAVRVLMDVVSAFVDPI   750
 751  SGVFANFQTLKSQNTEKEFLKFWESCWLFLDTIYKFTLKWASKYDYSELE   800
 801  NFTKDTLDLSRSLVDSFREFSDILHDQTKNLLLNVLETFKNMLYWLRLSD   850
 851  EVLLESCVRLIISTSDLAHEKHVKVDDSLVEMMAKYASKAKRFSNKLTEQ   900
 901  QASEILQKAKIFNKALTEEVATEAENYRKEKELSRLGKVIDLTDSVPASP   950
 951  SLSPSLSSTIASSSAESRADYLQRKALSSSITGRPRVAQPKITSFGTFQS  1000
1001  SANAKLHRTKPVKPLSKMELARMQLLNNRVVHPPSAPAFHTKSRGLSNKN  1050
1051  DDSSSEESDNDIESARELFAIAKAKGKGIQTVDINGKVVKRQTAAELAKQ  1100
1101  ELEHMRKRLNVDMNPLYEIILQWDYTRNSEYPDDEPIGNYSDVKDFFNSP  1150
1151  ADYQKVMKPLLLLESWQGLCSSRDREDYKPFSIIVGNRTAVSDFYDVYAS  1200
1201  VAKQVIQDCGISESDLIVMAYLPDFRPDKRLSSDDFKKAQHTCLAKVRTL  1250
1251  KNTKGGNVDVTLRIHRNHSFSKFLTLRSEIYCVKVMQMTTIEREYSTLEG  1300
1301  LEYYDLVGQILQAKPSPPVNVDAAEIETVKKSYKLNTSQAEAIVNSVSKE  1350
1351  GFSLIQGPPGTGKTKTILGIIGYFLSTKNASSSNVIKVPLEKNSSNTEQL  1400
1401  LKKQKILICAPSNAAVDEICLRLKSGVYDKQGHQFKPQLVRVGRSDVVNV  1450
1451  AIKDLTLEELVDKRIGERNYEIRTDPELERKFNNAVTKRRELRGKLDSES  1500
1501  GNPESPMSTEDISKLQLKIRELSKIINELGRDRDEMREKNSVNYRNRDLD  1550
1551  RRNAQAHILAVSDIICSTLSGSAHDVLATMGIKFDTVIIDEACQCTELSS  1600
1601  IIPLRYGGKRCIMVGDPNQLPPTVLSGAASNFKYNQSLFVRMEKNSSPYL  1650
1651  LDVQYRMHPSISKFPSSEFYQGRLKDGPGMDILNKRPWHQLEPLAPYKFF  1700
1701  DIISGRQEQNAKTMSYTNMEEIRVAIELVDYLFRKFDNKIDFTGKIGIIS  1750
1751  PYREQMQKMRKEFARYFGGMINKSIDFNTIDGFQGQEKEIILISCVRADD  1800
1801  TKSSVGFLKDFRRMNVALTRAKTSIWVLGHQRSLAKSKLWRDLIEDAKDR  1850
1851  SCLAYACSGFLDPRNNRAQSILRKFNVPVPSEQEDDYKLPMEYITQGPDE  1900
1901  VKSNKDTKKRRVVDEGEEADKAVKKKKKEKKKEKKKSKADDKKKNNKKAE  1950
1951  SPSTSSGTKKKSSIFGGMSVPSAVVPKTFPDVDSNKKAAAVVGKKKNNKH  2000
2001  VCFSDDVSFIPRNDEPEIKVTRSLSSVLKEKQLGLKETRTISPPEISNNE  2050
2051  DDDDEDDYTPSISDSSLMKSEANGRNNRVASHNQNFSASIYDDPQVSQAK  2100
2101  QTQVPAAITKHRSSNSVLSGGSSRILTASDYGEPNQNGQNGANRTLSQHV  2150
2151  GNANQYSTAPVGTGELHETLPAHPQDSYPAEAEDPYDLNPHPQPQSSAFK  2200
2201  GPGSGPTGTRNSSRRNASSSPFIPKKRKPRS                     2231

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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