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

NucPred

Fetching Q7RTP6 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MEERKHETMNPAHVLFDRFVQATTCKGTLKAFQELCDHLELKPKDYRSFY    50
  51  HKLKSKLNYWKAKALWAKLDKRGSHKDYKKGKACTNTKCLIIGAGPCGLR   100
 101  TAIDLSLLGAKVVVIEKRDAFSRNNVLHLWPFTIHDLRGLGAKKFYGKFC   150
 151  AGAIDHISIRQLQLILLKVALILGIEIHVNVEFQGLIQPPEDQENERIGW   200
 201  RALVHPKTHPVSEYEFEVIIGGDGRRNTLEGFRRKEFRGKLAIAITANFI   250
 251  NRNTTAEAKVEEISGVAFIFNQKFFQELREATGIDLENIVYYKDDTHYFV   300
 301  MTAKKQSLLDKGVILHDYADTELLLSRENVDQEALLSYAREAADFSTQQQ   350
 351  LPSLDFAINHYGQPDVAMFDFTCMYASENAALVREQNGHQLLVALVGDSL   400
 401  LEPFWPMGTGIARGFLAAMDSAWMVRSWSLGTSPLEVLAERESIYRLLPQ   450
 451  TTPENVSKNFSQYSIDPVTRYPNINVNFLRPSQVRHLYDTGETKDIHLEM   500
 501  ESLVNSRTTPKLTRNESVARSSKLLGWCQRQTDGYAGVNVTDLTMSWKSG   550
 551  LALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKE   600
 601  MASVGEPDKLSMVMYLTQFYEMFKDSLPSSDTLDLNAEEKAVLIASTRSP   650
 651  ISFLSKLGQTISRKRSPKDKKEKDLDGAGKRRKTSQSEEEEAPRGHRGER   700
 701  PTLVSTLTDRRMDVAVGNQNKVKYMATQLLAKFEENAPAQSIGIRRQGSM   750
 751  KKEFPQNLGGSDTCYFCQKRVYVMERLSAEGKFFHRSCFKCEYCATTLRL   800
 801  SAYAYDIEDGKFYCKPHYCYRLSGYAQRKRPAVAPLSGKEAKGPLQDGAT   850
 851  TDANGRANAVASSTERTPGSGVNGLEEPSIAKRLRGTPERIELENYRLSL   900
 901  RQAEALQEVPEETQAEHNLSSVLDTGAEEDVASSSSESEMEEEGEEEEEE   950
 951  PRLPPSDLGGVPWKEAVRIHALLKGKSEEELEASKSFGPGNEEEEEEEEE  1000
1001  YEEEEEEDYDEEEEESSEAGNQRLQQVMHAADPLEIQADVHWTHIREREE  1050
1051  EERMAPASESSASGAPLDENDLEEDVDSEPAEIEGEAAEDGDPGDTGAEL  1100
1101  DDDQHWSDSPSDADRELRLPCPAEGEAELELRVSEDEEKLPASPKHQERG  1150
1151  PSQATSPIRSPQESALLFIPVHSPSTEGPQLPPVPAATQEKSPEERLFPE  1200
1201  PLLPKEKPKADAPSDLKAVHSPIRSQPVTLPEARTPVSPGSPQPQPPVAA  1250
1251  STPPPSPLPICSQPQPSTEATVPSPTQSPIRFQPAPAKTSTPLAPLPVQS  1300
1301  QSDTKDRLGSPLAVDEALRRSDLVEEFWMKSAEIRRSLGLTPVDRSKGPE  1350
1351  PSFPTPAFRPVSLKSYSVEKSPQDEGLHLLKPLSIPKRLGLPKPEGEPLS  1400
1401  LPTPRSPSDRELRSAQEERRELSSSSGLGLHGSSSNMKTLGSQSFNTSDS  1450
1451  AMLTPPSSPPPPPPPGEEPATLRRKLREAEPNASVVPPPLPATWMRPPRE  1500
1501  PAQPPREEVRKSFVESVEEIPFADDVEDTYDDKTEDSSLQEKFFTPPSCW  1550
1551  PRPEKPRHPPLAKENGRLPALEGTLQPQKRGLPLVSAEAKELAEERMRAR  1600
1601  EKSVKSQALRDAMARQLSRMQQMELASGAPRPRKASSAPSQGKERRPDSP  1650
1651  TRPTLRGSEEPTLKHEATSEEVLSPPSDSGGPDGSFTSSEGSSGKSKKRS  1700
1701  SLFSPRRNKKEKKSKGEGRPPEKPSSNLLEEAAAKPKSLWKSVFSGYKKD  1750
1751  KKKKADDKSCPSTPSSGATVDSGKHRVLPVVRAELQLRRQLSFSEDSDLS  1800
1801  SDDVLEKSSQKSRREPRTYTEEELNAKLTRRVQKAARRQAKQEELKRLHR  1850
1851  AQIIQRQLQQVEERQRRLEERGVAVEKALRGEAGMGKKDDPKLMQEWFKL  1900
1901  VQEKNAMVRYESELMIFARELELEDRQSRLQQELRERMAVEDHLKTEEEL  1950
1951  SEEKQILNEMLEVVEQRDSLVALLEEQRLREREEDKDLEAAMLSKGFSLN  2000
2001  WS                                                  2002

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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