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

NucPred

Fetching Q80YV3 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MTRKFVKRSIFLHLLRHQPANAQIGLMEGNTFCTTLQPRLFTMDLNVVEH    50
  51  KVFYTELLNLCEAEDSALTKLPCYKSLPSLVPLRIAALNALAACNYLPQS   100
 101  REKIIAALFKALNSTNSELQEAGEACMRKFLEGATIEVDQIHTHMRPLLM   150
 151  MLGDYRSLTLNVVNRLTSVTRLFPNSFNDKFCDQMMQHLRKWMEVVVITH   200
 201  KGGQRSDGNEMKICSAIINLFHLIPAAPQTLVKPPLEVVMETERAMLIEA   250
 251  GSPFREPLIKFLTRHPSQTVELFMMGATLNDPQWSRMFMSFLKHKDARPL   300
 301  RDVLAANPNRFITLLLPGGAQTAVRPGSSSTSNMRLDLQFQAIKIISIIV   350
 351  KNDDAWLASQHSLVSQLRRVWVSETFQERHRKENMAATNWKEPKLLAFCL   400
 401  LNYCKRNYGDIELLFQLLRAFTGRFLCNMTFLKEYMEEEIPKNYSIAQKR   450
 451  ALFFRFVEFNDPNFGDELKAKVLQHILNPAFLYSFEKGEGEQLLGPPNPE   500
 501  GDNPESITSVFITKVLDPEKQADMLDSLRIYLLQYATLLVEHAPHHIHDN   550
 551  NKNRNSKLRRLMTFAWPCLLSKACVDPACRYSGHLLLAHIIAKFAIHKKI   600
 601  VLQVFHSLLKAHAMEARAIVRQAMAILTPAVPARMEDGHQMLTHWTRKII   650
 651  VEEGHTVPQLVHILHPIVQHFKVYYPVRHHLVQHMVSAMQRLGFTPSVTI   700
 701  EQRRLAVDLSEVVIKWELQRIKDQQPDSDMDPNSSGEGVNSVSIKRGLSV   750
 751  DSAQEVKRFRAATGAISAVFGRSQSLPGADSLLAKPIDKQHTDTVVNFLI   800
 801  RVACQVNDNTNTAGSPGEVLSRRCVNLLKTALRPDMWCKSELKLQWFDKL   850
 851  LMTVEQPNQVNYGNICTGLEVLNFLLTVLQSPAILSSFKPLQRGIAACMT   900
 901  CGNTKVLRAVHSLLSRLMSIFPTEPSTSSVASKYEELECLYAAVGKVIYE   950
 951  GLTNYEKATSANPSQLFGTLMIHKSACCNNPSYIDRLISVFMRSLQKMVR  1000
1001  EHLNPQTASGSTEATAAGTSELVMLSLDLVKTRLAVMSMEMRKNFIQTIL  1050
1051  TSLIEKSPDAKILRAVVKIVEEWVKNNSPMAANQTPTLREKSILLVKMMT  1100
1101  YIEKRFPEDLELNAQFLDLVNYVYRDEALSGSELTAKLEPAFLSGLRCAQ  1150
1151  PLIRAKFFEVFDNSMKRRVYERLLYVTCSQNWEAMGSHFWIKQCIELLLA  1200
1201  VCEKSTAIGTSCQGAMLPSITNVINLADSHDRAAFAMVTHVKQEPREREN  1250
1251  SESKEEDVEIDIELAPGDQTSTPKTKELSEKDIGNQLHMLTNRHDKFLDT  1300
1301  LREVKTGALLSAFVQLCHISTTLAEKTWVQLFPRLWKILSDRQQHALAGE  1350
1351  ISPFLCSGSHQVQRDCQPSALNCFVEAMSQCVPPIPMRPCVLKYLGKTHN  1400
1401  LWFRSTLMLEHQAFEKGLSLPIKPKQTTEFYEQESITPPQQEILDSLAEL  1450
1451  YSLLQEEDMWAGLWQKRCKFSETATAIAYEQHGFFEQAQESYEKAMDKAK  1500
1501  KEHERSNASPAIFPEYQLWEDHWIRCSKELNQWEALTEFGQSKGHINPYL  1550
1551  VLECAWRVSNWTAMKEALVQVEVSCPKEMAWKVNMYRGYLAICHPEEQQL  1600
1601  SFIERLVEMASSLAIREWRRLPHVVSHVHTPLLQAAQQIIELQEAAQINA  1650
1651  GLQPTNLGRNNSLHDMKTVVKTWRNRLPIVSDDLSHWSSVFMWRQHHYQA  1700
1701  IVTAYENSSHHDPSSNNAMLGVHASASAIIQYGKIARKQGLVNVALDILS  1750
1751  RIHTIPTVPIVDCFQKIRQQVKCYLQLAGVMGKNECMQGLEVIESTNLKY  1800
1801  FTKEMTAEFYALKGMFLAQINKSEEANKAFSAAVQMHDVLVKAWAMWGDY  1850
1851  LESIFVKERQLHLGVSAITCYLHACRHQNESKSRKYLAKVLWLLSFDDDK  1900
1901  NTLADAVDKYCIGVPPIQWLAWIPQLLTCLVGSEGKLLLNLISQVGRVYP  1950
1951  QAVYFPIRTLYLTLKIEQRERYKSDSGQQQPSSAGNQSHSASDPGPIRAT  2000
2001  APMWRCSRIMHMQRELHPTLLSSLEGIVDQMVWFRENWHEEVLRQLQQGL  2050
2051  AKCYSVAFEKSGAVSDAKITPHTLNFVKKLVSTFGVGLENVSNVSTMFSS  2100
2101  AASESLARRAQATAQDPVFQKLKGQFTTDFDFSVPGSMKLHNLISKLKKW  2150
2151  IKILEAKTKQLPKFFLIEEKCRFLSNFSAQTAEVEIPGEFLMPKPTHYYI  2200
2201  KIARFMPRVEIVQKHNTAARRLHIRGHNGKIYPYLVMNDACLTESRREER  2250
2251  VLQLLRLLNPCLEKRKETTKRHLFFTVPRVVAVSPQMRLVEDNPSSLSLV  2300
2301  EIYKQRCAKKGIEHDNPISRYYDRLATVQARGTQASHQVLRDILKEVQSN  2350
2351  MVPRSMLKEWALHTFPNATDYWTFRKMFTIQLALIGFAEFVLHLNRLNPE  2400
2401  MLQIAQDTGKLNVAYFRFDINDATGDLDANRPVPFRLTPNISEFLTTIGV  2450
2451  SGPLTASMIAVARCFAQPNFKVDGVLKTVLRDEIIAWHKKTQEDTSSPLS  2500
2501  AAGQPENMDSQQLVSLVQKAVTAIMTRLHNLAQFDGGESKVNTLVAAANS  2550
2551  LDNLCRMDPAWHPWL                                     2565

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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