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

NucPred

Fetching Q12053 from www.uniprot.org...

The NucPred score for your sequence is 0.47 (see score help below)

   1  MAQSRQLFLFGDQTADFVPKLRSLLSVQDSPILAAFLDQSHYVVRAQMLQ    50
  51  SMNTVDHKLARTADLRQMVQKYVDGKLTPAFRTALVCLCQLGCFIREYEE   100
 101  SGNMYPQPSDSYVLGFCMGSLAAVAVSCSRSLSELLPIAVQTVLIAFRLG   150
 151  LCALEMRDRVDGCSDDRGDPWSTIVWGLDPQQARDQIEVFCRTTNVPQTR   200
 201  RPWISCISKNAITLSGSPSTLRAFCAMPQMAQHRTAPIPICLPAHNGALF   250
 251  TQADITTILDTTPTTPWEQLPGQIPYISHVTGNVVQTSNYRDLIEVALSE   300
 301  TLLEQVRLDLVETGLPRLLQSRQVKSVTIVPFLTRMNETMSNILPDSFIS   350
 351  TETRTDTGRAIPASGRPGAGKCKLAIVSMSGRFPESPTTESFWDLLYKGL   400
 401  DVCKEVPRRRWDINTHVDPSGKARNKGATKWGCWLDFSGDFDPRFFGISP   450
 451  KEAPQMDPAQRMALMSTYEAMERAGLVPDTTPSTQRDRIGVFHGVTSNDW   500
 501  METNTAQNIDTYFITGGNRGFIPGRINFCFEFAGPSYTNDTACSSSLAAI   550
 551  HLACNSLWRGDCDTAVAGGTNMIYTPDGHTGLDKGFFLSRTGNCKPYDDK   600
 601  ADGYCRAEGVGTVFIKRLEDALADNDPILGVILDAKTNHSAMSESMTRPH   650
 651  VGAQIDNMTAALNTTGLHPNDFSYIEMHGTGTQVGDAVEMESVLSVFAPS   700
 701  ETARKADQPLFVGSAKANVGHGEGVSGVTSLIKVLMMMQHDTIPPHCGIK   750
 751  PGSKINRNFPDLGARNVHIAFEPKPWPRTHTPRRVLINNFSAAGGNTALI   800
 801  VEDAPERHWPTEKDPRSSHIVALSAHVGASMKTNLERLHQYLLKNPHTDL   850
 851  AQLSYTTTARRWHYLHRVSVTGASVEEVTRKLEMAIQNGDGVSRPKSKPK   900
 901  ILFAFTGQGSQYATMGKQVYDAYPSFREDLEKFDRLAQSHGFPSFLHVCT   950
 951  SPKGDVEEMAPVVVQLAITCLQMALTNLMTSFGIRPDVTVGHSLGEFAAL  1000
1001  YAAGVLSASDVVYLVGQRAELLQERCQRGTHAMLAVKATPEALSQWIQDH  1050
1051  DCEVACINGPEDTVLSGTTKNVAEVQRAMTDNGIKCTLLKLPFAFHSAQV  1100
1101  QPILDDFEALAQGATFAKPQLLILSPLLRTEIHEQGVVTPSYVAQHCRHT  1150
1151  VDMAQALRSAREKGLIDDKTLVIELGPKPLISGMVKMTLGDKISTLPTLA  1200
1201  PNKAIWPSLQKILTSVYTGGWDINWKKYHAPFASSQKVVDLPSYGWDLKD  1250
1251  YYIPYQGDWCLHRHQQDCKCAAPGHEIKTADYQVPPESTPHRPSKLDPSK  1300
1301  EAFPEIKTTTTLHRVVEETTKPLGATLVVETDISRKDVNGLARGHLVDGI  1350
1351  PLCTPSFYADIAMQVGQYSMQRLRAGHPGAGAIDGLVDVSDMVVDKALVP  1400
1401  HGKGPQLLRTTLTMEWPPKAAATTRSAKVKFATYFADGKLDTEHASCTVR  1450
1451  FTSDAQLKSLRRSVSEYKTHIRQLHDGHAKGQFMRYNRKTGYKLMSSMAR  1500
1501  FNPDYMLLDYLVLNEAENEAASGVDFSLGSSEGTFAAHPAHVDAITQVAG  1550
1551  FAMNANDNVDIEKQVYVNHGWDSFQIYQPLDNSKSYQVYTKMGQAKENDL  1600
1601  VHGDVVVLDGEQIVAFFRGLTLRSVPRGALRVVLQTTVKKADRQLGFKTM  1650
1651  PSPPPPTTTMPISPYKPANTQVSSQAIPAEATHSHTPPQPKHSPVPETAG  1700
1701  SAPAAKGVGVSNEKLDAVMRVVSEESGIALEELTDDSNFADMGIDSLSSM  1750
1751  VIGSRFREDLGLDLGPEFSLFIDCTTVRALKDFMLGSGDAGSGSNVEDPP  1800
1801  PSATPGINPETDWSSSASDSIFASEDHGHSSESGADTGSPPALDLKPYCR  1850
1851  PSTSVVLQGLPMVARKTLFMLPDGGGSAFSYASLPRLKSDTAVVGLNCPY  1900
1901  ARDPENMNCTHGAMIESFCNEIRRRQPRGPYHLGGWSSGGAFAYVVAEAL  1950
1951  VNQGEEVHSLIIIDAPIPQAMEQLPRAFYEHCNSIGLFATQPGASPDGST  2000
2001  EPPSYLIPHFTAVVDVMLDYKLAPLHARRMPKVGIVWAADTVMDERDAPK  2050
2051  MKGMHFMIQKRTEFGPDGWDTIMPGASFDIVRADGANHFTLMQKEHVSII  2100
2101  SDLIDRVMA                                           2109

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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