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

NucPred

Fetching Q8CJ19 from www.uniprot.org...

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

   1  MEERKQETTNQAHVLFDRFVQATTCKGTLRAFQELCDHLELKPKDYRSFY    50
  51  HKLKSKLNYWKAKALWAKLDKRGSHKDYKKGKACTNTKCLIIGAGPCGLR   100
 101  TAIDLSLLGAKVVVIEKRDAFSRNNVLHLWPFTIHDLRGLGAKKFYGKFC   150
 151  AGAIDHISIRQLQLILLKVALILGIEIHVNVEFQGLVQPPEDQENERIGW   200
 201  RALVHPKTHPVSEYEFEVIIGGDGRRNTLEGFRRKEFRGKLAIAITANFI   250
 251  NRNTTAEAKVEEISGVAFIFNQKFFQELREATGIDLENIVYYKDDTHYFV   300
 301  MTAKKQSLLDKGVILHDYTDTELLLSRENVDQEALLNYAREAADFSTQQQ   350
 351  LPSLDFAINHYGQPDVAMFDFTCMYASENAALVREQNGHQLLVALVGDSL   400
 401  LEPFWPMGTGIARGFLAAMDSAWMVRSWSLGTSPLEVLAERESIYRLLPQ   450
 451  TTPENVSKNFSQYSIDPVTRYPNININFLRPSQVRHLYDSGETKDIHLEM   500
 501  ENMVNPRTTPKLTRNESVARSSKLLGWCQRQTEGYSGVNVTDLTMSWKSG   550
 551  LALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKE   600
 601  MASVGEPDKLSMVMYLTQFYEMFKDSLSSSDTLDLNAEEKAVLIASTKSP   650
 651  ISFLSKLGQTISRKRSPKDKKEKDSDGAGKRRKTSQSEEEEPPRSYKGER   700
 701  PTLVSTLTDRRMDAAVGNQNKVKYMATQLLAKFEENAPAQSTGVRRQGSI   750
 751  KKEFPQNLGGSDTCYFCQKRVYVMERLSAEGKFFHRSCFKCEYCATTLRL   800
 801  SAYAYDIEDGKFYCKPHYCYRLSGYAQRKRPAVAPLSGKEVKGALQDGPT   850
 851  ADANGLASVAASSAERSPGTSMNGLEEPSIAKRLRGTPERIELENYRRSV   900
 901  RQVEELEEVPEETQAEHNLSSVLDKGTEEDVASSSSESEMEEEEEEDDED   950
 951  DHLPTSDLGGVPWKEAVRIHALLKGRSEEELEASKNFEPEEEEEEEEYEE  1000
1001  EDEEYEEEEEEESSEAGNKRLQQIITAADPLAIQADVHWTHIREREAEER  1050
1051  MLPTSESSTSRAPLDEDDLEEDADSEPAETEGEAAEDGDPGDTGAELDDQ  1100
1101  HWSDDIPSDAEAEHRLQSQAKVKAELELRVSENEEEKPSDAPKQEERGTS  1150
1151  QVSSPSQPPEKQVGVFSPARSPGTEEAKSPLATKVKSPEEPLFPTPLLLR  1200
1201  EKPKAEVPEEQKAVLSPIRSQPVALPEARSPTSPTSLQPESLLAPPTPPT  1250
1251  PPPTQLPICSQPQPSSDASIPSPTKSPIRFQPVPAKTSTPLTPLPVKSQG  1300
1301  DPKDRLSGPLAVEEVLKRSDLVEEFWMKSAEIRRSLGLTPVDRSKGSEPS  1350
1351  LPSPASKPISLKSYSVDKSPQDEGLCLLKPPSVPKRLGLPKSAGDQPPLL  1400
1401  TPKSPSDKELRSSQEERRDLSSSSGLGLHDSSSNMKTLGSQSFNTSDSTM  1450
1451  LTPPSSPPPPPPPNEEPATLRRKPHQTFERREASIIPPPTPASFMRPPRE  1500
1501  PAQPPREEVRKSFVESVDEIPFADDVEDTYDDKTEDSSLQEKFFTPPSCW  1550
1551  SRSEKLQAKENGRLPPLEQDVPPQKRGLPLVSAEAKELAEERMRAREKSV  1600
1601  KSQALRDAMAKQLSRMQAMEMVSSRSHTAQSQGKELGSESTRHPSLRGTQ  1650
1651  EPTLKHEATSEEILSPPSDSGGPDGSVTSSEGSSGKSKKRSSLFSPRRNK  1700
1701  KEKKTKGEARPPEKPSPGLPEDVVAKPKSLWKSVFSGYKKDKKKKSDEKS  1750
1751  CSSTPSSGATVDSGQRRASPMVRAELQLRRQLSFSEDSDLSSDDILERSS  1800
1801  QKSKREPRTYTEEELSAKLTRRVQKAARRQAKQEELKRLHRAQIIQRQLE  1850
1851  QVEEKQRQLEERGVAVEKALRGEAGMGKKDDPKLMQEWFKLVQEKNAMVR  1900
1901  YESELMIFARELELEDRQSRLQQELRERMAVEDHLKTEGELSEEKKILNE  1950
1951  MLEVVEQRDSLVALLEEQRLREKEEDKDLEAAMLCKGFSLDWS         1993

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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