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

NucPred

Fetching Q03460 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MSNSLSLTFTALNNPQINAISNPNARLRPLARVTRCSATCVERKRWLGTK    50
  51  LRSGGGLERIQLWESGGLGRLPKLRVAVKSSFSAVPDKPMGLYDPAFDKD   100
 101  SCGVGFVAELNGQSSRKTVTDALEMLVRMTHRGACGCEANTGDGAGILVA   150
 151  LPHGFYQEVVDFQLPPQGNYAVGMFFLPKSDSRRKESKNIFTKVAESLGH   200
 201  KVLGWRSVPTDNTGLGKSAQLTEPVIEQVFLTPSSDSKVDLEKQMYILRK   250
 251  LSMVSITSALNLQSDGITDFYICSLSSRTVIYKGQLTPAQLGEYYYADLG   300
 301  NERFTSYMALIHSRFSTNTFPSWDRAQPFRVLGHNGEINTLRGNVNWIKA   350
 351  REGLLKCKELGLSENDLKKFLPIVDANSSDSGCFDGVLEFLLHSGKSLPE   400
 401  AVMMMIPEAWQNDKNMDPQRKAFYEYYSALMEPWDGPALISFTDGHYLGA   450
 451  TLDRNGLRPGRFYVTHSGRVIMASEVGVVDIPPEDVCRKGRLNPGMMLLV   500
 501  DFEKQIVVNDDALKEQYSLARPYGDWLEKQKIELKDIIDSVHESDIVPPT   550
 551  ISGVPPLSNDDVDMENMGIQGLLAPLKAFGYSVESLEILLLPMAKDGVEA   600
 601  LGSMGNDTPLAVMSNREKLTFEYFKQMFAQVTNPPIDPIREKIVTSMRCM   650
 651  VGPEGDLTETTEEQCHRLSLKGPLLSTKEMEAIKKMNYRGWRSKVIDITY   700
 701  SKERGTKGLEEALDRICTEAHNAISEGYTTLVLSDRAFSKKHVAVSSLLA   750
 751  VGAVHQHLVKTLERTRVALMVESAEPREVHHFCTLVGFGADAICPYLAIE   800
 801  AIWRLQVDGKIPPKASGDFNSKDELVKKYFKASTYGMMKVLAKMGISTLA   850
 851  SYKGAQIFEALGLSSEVIEKCFAGTPSRVEGATFEMLAQDALHLHELAFP   900
 901  SRIFSPGSAEAVALPNPGDYHWRKGGEVHLNDPLAIAKLQEAARTNSVDA   950
 951  YKQYSKTIHELNKACNLRGLLKFKDAASKVPISEVEPASEIVKRFCTGAM  1000
1001  SYGSISLEAHTALATAMNTIGGKSNTGEGGEQPSRMEPLADGSRNPKRSA  1050
1051  IKQVASGRFGVSSYYLTNADELQIKMAQGAKPGEGGELPGHKVIGDIAIT  1100
1101  RNSTAGVGLISPPPHHDIYSIEDLAQLIHDLKNANPAARISVKLVSEAGV  1150
1151  GVIASGVVKGHAEHVLISGHDGGTGASRWTGIKSAGLPWELGLAETHQTL  1200
1201  VANDLRGRTTLQTDGQLKTGRDVAIAALLGAEEYGFSTAPLITLGCIMMR  1250
1251  KCHKNTCPVGIATQDPVLREKFAGEPEHVINFFFMVAEEMREIMSQLGFR  1300
1301  TVNEMVGRSDMLEVDKEVVKGNAKLENIDLSLLLRPAAELRPEAAQYCVQ  1350
1351  KQDHGLDMALDNKLISLSNAALEKGLPVYIETPICNTNRAVGTMLSHEVT  1400
1401  KRYNLAGLPADTIHIQFTGSAGQSFGAFLCPGITLELEGDSNDYIGKGLS  1450
1451  GGKVVVYPPKGSNFDPKDNILIGNVALYGATRGEAYFNGMAAERFCVRNS  1500
1501  GALAVVEGVGDHGCEYMTGGTVVVLGKTGRNFAAGMSGGIAYVLDVDGTF  1550
1551  QSRCNLELVDLDKVEEEEDIITLRMLIQQHQRHTNSLLAKEVLVDFENLL  1600
1601  PKFVKVFPREYKRVLASMKSDAASKDAVERAAEDVDEQDDEAQAVEKDAF  1650
1651  EELKKLATASLNEKPSEAPKRPSQVTDAVKHRGFVAYEREGVQYRDPNVR  1700
1701  LNDWNEVMMETKPGPLLKTQSARCMDCGTPFCHQENSGCPLGNKIPEFNE  1750
1751  LVYQNRWQEALERLLETNNFPEFTGRVCPAPCEGSCVLGIIENPVSIKNI  1800
1801  ECAIIDKAFEEGWMIPRPPVKRTGKRVAIVGSGPSGLAAADQLNKMGHIV  1850
1851  TVFERADRIGGLMMYGVPNMKTDKVDIVQRRVNLMAEEGINFVVNANIGL  1900
1901  DPLYSLERLREENDAIVLAVGATKPRDLPVPGRELSGVHFAMEFLHANTK  1950
1951  SLLDSNLQDGNYISAKGKKVVVIGGGDTGTDCIGTSIRHGCTAVVNLELL  2000
2001  PQPPPTRAPGNPWPQWPRIFRVDYGHQEAETKFGKDPRTYEVLTKRFVGD  2050
2051  ENGVVKGLEVVRVCWEKDETGKFQFKEIEGSEEIIEADLVLLAMGFLGPE  2100
2101  ATIAEKLGVERDNRSNFKADYGRFSTSVDGVFAAGDCRRGQSLVVWAISE  2150
2151  GRQAAAQVDSYLTNEDHGIDGNQDEFVKRQQDLNKKHSKHTVMT        2194

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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