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

NucPred

Fetching Q5XG71 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MKPKPLSHKTENTYRFLTFAERLGNVNIDIIHRIDRTASYDEDVETYFFE    50
  51  ALLKWRELNLTEHFGKFYKEVIDKCQSFNQLVYHQNEIVQSLKTHLQIRN   100
 101  SLAYQPLLDLVVQLARDLQTDFYPHFEDFFLTITSILETQDTELLEWAFT   150
 151  SLSYLYKYLWRLMVKDMSKIYSLYSTLLAHKKLHIRNFAAESFTFLMRKV   200
 201  SDKNALFNLMFLDLNEHPEKVEGVGQLLFEMCKGVRNMFHSCTGQALKLL   250
 251  LQKLGPVTETETQLPWILVGETLKTMAKSSVVYIYKEHFGVFFDCLQESL   300
 301  LELHNKVTEANCCENSEQMRRLLETYLIVVKHGSGSKITRPADVCGVLSE   350
 351  ALQTASLSTSCRKTLLDVVSALLLAENVSLPETLIKETVEKVFESKFERR   400
 401  SVLDFSEVMFAMKQFEQLFLPSFLLYIENCFLMDNSVVSDEALAILAKLI   450
 451  LHKAPPPTAGSMAIEKYPLVFSQQTVGSYLKQRKADSKRRKEQFPVLSHL   500
 501  LSIVQLPPNKDATYLSRSWAALVVLPHLRPLEKEKTISLVSCFIESLFLA   550
 551  VDRGSFGKGHLFVLCQAVNTLLSLEESSELLHLVPVGRVKHLVLTSPTEP   600
 601  SVLLLADLYYQRLALCGCKGPLSEEALMELFPKLQANISTGVSKIRLLTI   650
 651  RILNHFDIRLPVSMEDDGLSERQSAFAILRQAELVPATVSDYREKLLHLR   700
 701  KLRHDVVQGAVPQGRLQEVPLRYLLGMLYVNFSALWDPVIELISSHAYGM   750
 751  ENKQFWNVCYEHLEKAASHAEKELHKDVRDEESTGDESWEQTQEGDVGDL   800
 801  YQQQLALKTDCRERLDHTNFRFLLWRALAKFPERVEPRSRELSPLFLRFI   850
 851  NNEYYPADLQVAPTQDLRKKGRGAVAEEEEEEEPAAGEDEELEEEAVPTE   900
 901  DAPQKKKTRRAAAKQLIAHLQVFSKFSNPRALYLESKLYELYLQLLLHQD   950
 951  QAVQKITLDCIMTYRHPHILPYRENLQRLLDDRSFKEEIVHFNISEDNTV  1000
1001  VKAAHRADLFPILMRILYGRMKNKTGSKTQGKSASGTRMAIVLRFLAGTQ  1050
1051  PEEIQLFLDLLSEPVKHFKDGDCCSAVIQAVEDLDVSKVLPVGRQHGVLN  1100
1101  SLEVVLKNISHLISTYLPKILQILLCMTATVSHILDQREKIQLRFINPLK  1150
1151  NLRRLGIKMVTDIFLDWESYQFKAEEIDAVFHGTVWPQICRLGSESQYSP  1200
1201  TPLLKLISIWSRNARYFPLLAKQKPGHPEYDILTNVFAVLSAKNLSEATA  1250
1251  SIIMDIVDDLLNLPDFQPTEAVPSLPVTGCVYADVAEDTEPVTVGGRLVL  1300
1301  PHVPAILQYLSKTTISAEKVKKKKNRAQVSKELGILSKISKFMKDREQCS  1350
1351  LLITLLLPFLLRGNVAQDTELDILVTVQNLLQHCLHPAHFLRPLAKLFSV  1400
1401  IKNKLSRQLLCTVFQMSDFESRLKYITDIVKLNAFDKRHLDDINFDVRFS  1450
1451  AFQTITSNIKAMQTVDADYLIAVMHNCFYNMEIGDMSLSDNASICLTSII  1500
1501  KRLAALNVTEKEYKEIIHRTLLEKLRKGLKSQTESVQHDYTLILSCLIQT  1550
1551  FPNQLEFKDLVQLTHCHDPEMDFFENMKHIQIHRRARALKKLAKQLLEGQ  1600
1601  VVLSSKSLQNYIMPYAMAPILDEKMLKHENITIAATEVIGAICRHLSWPA  1650
1651  YVYYLKHFIHVLQSGQINQKLAVSLLVIVLEAFHFDYKTLEEQMGNVKNE  1700
1701  ENTVEMAELLEPEAMEVEDMDEAGKEQASERLSDSKEALGAPEAAASEGT  1750
1751  VAKEQECISKSVSFLPRNKEELERTIQTIQGAITGDILPRLHKCLASATK  1800
1801  REEEHKLVKSKVVNDEEVVRVPLAFAMVKLMRSLPREVMEANLPSILLKV  1850
1851  CVLLKNRAQEIRDIARSTLSKIIEDLGVHFLQYVLKELQTTLVRGYQVHV  1900
1901  LTFTVYTLLQGLSSKLQVGDLDSCLHIMTEIFNHELFGALAEEKEVKQIL  1950
1951  SKVMEARRSKSYDSYEILGKFVGKQQVTKLILPLKEILQNTTSLKLARKV  2000
2001  HETLRRIIAGLIVNPDMTADALLLLSYGLVSENLPLLTEKEKKPAAPVPD  2050
2051  ARLPPQSCLLLPATPVRGGPKAVVNKKTNMHIFIESGLRLLHLSLKTSRI  2100
2101  KSSSEHVLEMLDPFVSVLINCLGAQDVKVITGALQCLIWVLRFPLPSIAS  2150
2151  KAEQLTKHLFLLLKNYARVGAARGQNFHLVVNCFKCVTIVVKKVKSHQIT  2200
2201  EKQLQVLLAYAEEDIYDTSRQATAFGLLKAILSRKLLVPEIDDIMRKVSK  2250
2251  LAISAQNEPARVQCRQVFLKYILDYPLGEKLRPNLEFMLAQLNYEHETGR  2300
2301  ESTLEMIAYLFETFPQGLLHEHCGMFFIPLCLMMVNDDSAMCKRMASMAI  2350
2351  KSLLSKVDREKKDWLFGLVTSWFEAKKRLNRQLAALACGLFVESEGVDFE  2400
2401  RRLGTLLPVIEKEIDPENFKDIIEETEEKAADRLLFGFLTLMRKLIKECS  2450
2451  IIHFTKPSETLSKIWSHVHSHLRHPHSWVWLTAAQIFGLLFASCQPEELI  2500
2501  QKWKGKKTKKKTSDPIAVRFLTSDLGQKMKSISLASCHQLHSKFLDESLG  2550
2551  EQVVKNLLFIAKVLYLLELESGNKRGEVKDSEEQDTLADALAREAAEEKA  2600
2601  GAGGKMESNREKKEEPSKPATLMWLIQKLSRMAKLEAAYSPRNPLKRTCI  2650
2651  FKFLGAVAVDLGVDRVKPYLPLIIAPLFRELNSTFAEQDPVLKNLSQEII  2700
2701  ELLKKLVGLESFSLAFASVQKQASEKRALRKKRKALEFVTNPDIAAKKKL  2750
2751  KKHKNKSEAKKRKIEFLRPGYKAKRQKSHSLRDLAMVE              2788

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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