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

NucPred

Fetching P91620 from www.uniprot.org...

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

   1  MEQKCIRRKGSVRLTEPTGHAHVRIEQRPQLPPRRQKSAEEVATMPKSAL    50
  51  RQPPEQLEWFDRRAQQRHSARSAEGGQVREETMEWLKLQKTASPIQPVRT   100
 101  SSGPSEITVLKDELPDWLLDHLPRKKERERDRLPSDADKAVGSAYAKALA   150
 151  DLLKKPLSRQGSGPCEFSLLKTDIVEWLTKMQSSSGTDRGKSRRSHHRRN   200
 201  GSGGDAQPRSNSQEDAQDQSKTSHRKRHSLGHSGAVSEEEQQQLTADWIA   250
 251  YPLHKLQSLGKQPPPAQPPERMSIPSGYAVPSALSHTPLCQRREERSRER   300
 301  RLRHSASEVVGSGGAGAASTSNTAHLERLYAKPHKERYQYVPKTKESSGR   350
 351  KERSRRHQTQRSATVSDMSAQRSGGHKRKSSSAERAPRSPSPGPCTDPDC   400
 401  PLLPICTDPHCRYQECQARQCITSSVSSVNLARHQQLAQVQLHAVPAHLV   450
 451  GAMGSDVPTTPSTTATPPPPTGGGTMGVGATGAGAGATSERRLVICHDCR   500
 501  SCAPLLSCRNRKCLNAAKCNSLPRCAADFNRLRTQLSQPPTTLDDIEPAP   550
 551  LDDLEMQPLPSPPHPHPHHHYRSNSQPNTLQRGDSASSAGMGAGVGGAGH   600
 601  GGLGGPGSGLAWLEPTTTLVQPLPAYVHHSNGKLMKSASAASLNSRRRRH   650
 651  KTVHFGENLLREVCQNRKLIKTEAQVPSGSAPMKANIQMLYNFVEGVLSA   700
 701  WVDDDEDQVRSGAESEPEHGVVPMQPIHRCNRLRYQCIRRVVEEAADLQG   750
 751  TLKLGNSRYRHRHWRSTAKQCNEMFLRKISDDDRMSLTTAVSDEDDGESV   800
 801  MASPYKAKATGTAASSFNCTGAVRKAGFLSVKKWLLRKKHQIELARKRGW   850
 851  KGYWVCLKGTTLLFYPCDSREGRSVEAAPKHLIIVDGAIMQPIPEHPKRD   900
 901  YIFCLSTAFGDAYLFQAPCQVELENWVNSIHSACAAAFARHRGKTGTLHL   950
 951  LQEEIFRLEKAIESDHKLKHMAELQQSVVTDQETRHQIQTQILQWEENLE  1000
1001  RLHCEQFRLRCYMASLQSGELPNPKSLLTHVSRPTKNTLNKLGVFTVSSF  1050
1051  HAFICARSPSLLNNLLAGRGATKRRPPMLSRSNSGSSRRSMQMNSRDEPE  1100
1101  KTFKVAMPDNAYSTVYLRDAMSVEEFLASACARRNLNPMEHFVRVKKRRD  1150
1151  MEDHNYFVPHRNDLIENYLHNHEFVEVCMKILYQVELQRTTLEQMWGFSV  1200
1201  EAELIENAERQDELCCYVSRVEDKSVAMHNGIIKGDEIMVINGAIVSDLD  1250
1251  MMYLESVLQEEQSLSMMMRSSRTEPPDLVGIMRVTDDMIDSLVCPPPPTD  1300
1301  PPVMSEEMITGLIVPAPGWNGTSKDLYSPEAESSPATSFVDPAAMAAQLA  1350
1351  VGGVGGVVVGGLGVAKPTSRTSSFEIENLLKTAEQVTGFCRSPQETRKSS  1400
1401  PTGSVTSSVSTTALTPSRQLTDAEKLRKVVMELVDTERTYVKHLNNLLEH  1450
1451  YLEPMKRETFLSNAEINALFGNIHEIVTFQRQFLQNLEESLDLEPDFNKF  1500
1501  EHCGQFRNVLFAIGSAFLYYVNHFKLYSSFCASHSKAQKVLHPNEGNHAL  1550
1551  QEFLAARNPKQQHSSTLESYLIKPIQRILKYPLLLQQMRNLTDTRADEHV  1600
1601  HLCEALKGMEKVAEHINEMQRIHEEYGAIFDHLFRQHQKSCKQPIDLSPG  1650
1651  DLLYYGGVEWLNISDFLGKIKKGLELHAMCFVFKSAVVFLCKERLRQKKK  1700
1701  LMGVSSKNATNEVEIIRYQVLIPVTEVQVRASSAKDMDSHFLWELIHLRS  1750
1751  QLQRRSEKVYVLSNSTADFRNAFLKTIRQIIRESVRNMSIPMKNFGGSSG  1800
1801  SVSGHSSQGMGSMGYPGNSQTLERPKQQITIVHGSHTLGKPKKKSGSQRH  1850
1851  SAGNIDYDNLSGSQEADDLPPSVGVVHYASGHTHGQQMQPAGFRGRSKTV  1900
1901  GDVTEITCSSPEPHQQQQQQQQQQQQLMQQGHAHAHPHPHPHPREPPPPP  1950
1951  IRQPHLHHHSSDIERIDPGTKSEGEEDSQQGTIRPKATLGRTPNHLTLST  2000
2001  TSTLSVGSTGSQARLIQSSHPPASYQPVLMKDLGSPVWKPRDMINLGTDP  2050
2051  QSTTRKDDVKN                                         2061

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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