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

NucPred

Fetching Q96BY7 from www.uniprot.org...

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

   1  MPWPFSESIKKRACRYLLQRYLGHFLQEKLSLEQLSLDLYQGTGSLAQVP    50
  51  LDKWCLNEILESADAPLEVTEGFIQSISLSVPWGSLLQDNCALEVRGLEM   100
 101  VFRPRPRPATGSEPMYWSSFMTSSMQLAKECLSQKLTDEQGEGSQPFEGL   150
 151  EKFAETIETVLRRVKVTFIDTVLRIEHVPENSKTGTALEIRIERTVYCDE   200
 201  TADESSGINVHQPTAFAHKLLQLSGVSLFWDEFSASAKSSPVCSTAPVET   250
 251  EPKLSPSWNPKIIYEPHPQLTRNLPEIAPSDPVQIGRLIGRLELSLTLKQ   300
 301  NEVLPGAKLDVDGQIDSIHLLLSPRQVHLLLDMLAAIAGPENSSKIGLAN   350
 351  KDRKNRPMQQEDEYRIQMELNRYYLRKDSLSVGVSSEQSFYETETARTPS   400
 401  SREEEVFFSMADMDMSHSLSSLPPLGDPPNMDLELSLTSTYTNTPAGSPL   450
 451  SATVLQPTWGEFLDHHKEQPVRGSTFPSNLVHPTPLQKTSLPSRSVSVDE   500
 501  SRPELIFRLAVGTFSISVLHIDPLSPPETSQNLNPLTPMAVAFFTCIEKI   550
 551  DPARFSTEDFKSFRAVFAEACSHDHLRFIGTGIKVSYEQRQRSASRYFST   600
 601  DMSIGQMEFLECLFPTDFHSVPPHYTELLTFHSKEETGSHSPVCLQLHYK   650
 651  HSENRGPQGNQARLSSVPHKAELQIKLNPVCCELDISIVDRLNSLLQPQK   700
 701  LATVEMMASHMYTSYNKHISLHKAFTEVFLDDSHSPANCRISVQVATPAL   750
 751  NLSVRFPIPDLRSDQERGPWFKKSLQKEILYLAFTDLEFKTEFIGGSTPE   800
 801  QIKLELTFRELIGSFQEEKGDPSIKFFHVSSGVDGDTTSSDDFDWPRIVL   850
 851  KINPPAMHSILERIAAEEEEENDGHYQEEEEGGAHSLKDVCDLRRPAPSP   900
 901  FSSRRVMFENEQMVMPGDPVEMTEFQDKAISNSHYVLELTLPNIYVTLPN   950
 951  KSFYEKLYNRIFNDLLLWEPTAPSPVETFENISYGIGLSVASQLINTFNK  1000
1001  DSFSAFKSAVHYDEESGSEEETLQYFSTVDPNYRSRRKKKLDSQNKNSQS  1050
1051  FLSVLLNINHGLIAVFTDVKQDNGDLLENKHGEFWLEFNSGSLFCVTKYE  1100
1101  GFDDKHYICLHSSSFSLYHKGIVNGVILPTETRLPSSTRPHWLEPTIYSS  1150
1151  EEDGLSKTSSDGVGGDSLNMLSVAVKILSDKSESNTKEFLIAVGLKGATL  1200
1201  QHRMLPSGLSWHEQILYFLNIADEPVLGYNPPTSFTTFHVHLWSCALDYR  1250
1251  PLYLPIRSLLTVETFSVSSSVALDKSSSTLRIILDEAALHLSDKCNTVTI  1300
1301  NLSRDYVRVMDMGLLELTITAVKSDSDGEQTEPRFELHCSSDVVHIRTCS  1350
1351  DSCAALMNLIQYIASYGDLQTPNKADMKPGAFQRRSKVDSSGRSSSRGPV  1400
1401  LPEADQQMLRDLMSDAMEEIDMQQGTSSVKPQANGVLDEKSQIQEPCCSD  1450
1451  LFLFPDESGNVSQESGPTYASFSHHFISDAMTGVPTENDDFCILFAPKAA  1500
1501  MQEKEEEPVIKIMVDDAIVIRDNYFSLPVNKTDTSKAPLHFPIPVIRYVV  1550
1551  KEVSLVWHLYGGKDFGIVPPTSPAKSYISPHSSPSHTPTRHGRNTVCGGK  1600
1601  GRNHDFLMEIQLSKVKFQHEVYPPCKPDCDSSLSEHPVSRQVFIVQDLEI  1650
1651  RDRLATSQMNKFLYLYCSKEMPRKAHSNMLTVKALHVCPESGRSPQECCL  1700
1701  RVSLMPLRLNIDQDALFFLKDFFTSLSAEVELQMTPDPEVKKSPGADVTC  1750
1751  SLPRHLSTSKEPNLVISFSGPKQPSQNDSANSVEVVNGMEEKNFSAEEAS  1800
1801  FRDQPVFFREFRFTSEVPIRLDYHGKHVSMDQGTLAGILIGLAQLNCSEL  1850
1851  KLKRLSYRHGLLGVDKLFSYAITEWLNDIKKNQLPGILGGVGPMHSLVQL  1900
1901  VQGLKDLVWLPIEQYRKDGRIVRGFQRGAASFGTSTAMAALELTNRMVQT  1950
1951  IQAAAETAYDMVSPGTLSIEPKKTKRFPHHRLAHQPVDLREGVAKAYSVV  2000
2001  KEGITDTAQTIYETAAREHESRGVTGAVGEVLRQIPPAVVKPLIVATEAT  2050
2051  SNVLGGMRNQIRPDVRQDESQKWRHGDD                        2078

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.)

Go back to the NucPred Home Page.