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

NucPred

Fetching Q9UHV7 from www.uniprot.org...

The NucPred score for your sequence is 0.93 (see score help below)

   1  MSASFVPNGASLEDCHCNLFCLADLTGIKWKKYVWQGPTSAPILFPVTEE    50
  51  DPILSSFSRCLKADVLGVWRRDQRPGRRELWIFWWGEDPSFADLIHHDLS   100
 101  EEEDGVWENGLSYECRTLLFKAVHNLLERCLMNRNFVRIGKWFVKPYEKD   150
 151  EKPINKSEHLSCSFTFFLHGDSNVCTSVEINQHQPVYLLSEEHITLAQQS   200
 201  NSPFQVILCPFGLNGTLTGQAFKMSDSATKKLIGEWKQFYPISCCLKEMS   250
 251  EEKQEDMDWEDDSLAAVEVLVAGVRMIYPACFVLVPQSDIPTPSPVGSTH   300
 301  CSSSCLGVHQVPASTRDPAMSSVTLTPPTSPEEVQTVDPQSVQKWVKFSS   350
 351  VSDGFNSDSTSHHGGKIPRKLANHVVDRVWQECNMNRAQNKRKYSASSGG   400
 401  LCEEATAAKVASWDFVEATQRTNCSCLRHKNLKSRNAGQQGQAPSLGQQQ   450
 451  QILPKHKTNEKQEKSEKPQKRPLTPFHHRVSVSDDVGMDADSASQRLVIS   500
 501  APDSQVRFSNIRTNDVAKTPQMHGTEMANSPQPPPLSPHPCDVVDEGVTK   550
 551  TPSTPQSQHFYQMPTPDPLVPSKPMEDRIDSLSQSFPPQYQEAVEPTVYV   600
 601  GTAVNLEEDEANIAWKYYKFPKKKDVEFLPPQLPSDKFKDDPVGPFGQES   650
 651  VTSVTELMVQCKKPLKVSDELVQQYQIKNQCLSAIASDAEQEPKIDPYAF   700
 701  VEGDEEFLFPDKKDRQNSEREAGKKHKVEDGTSSVTVLSHEEDAMSLFSP   750
 751  SIKQDAPRPTSHARPPSTSLIYDSDLAVSYTDLDNLFNSDEDELTPGSKK   800
 801  SANGSDDKASCKESKTGNLDPLSCISTADLHKMYPTPPSLEQHIMGFSPM   850
 851  NMNNKEYGSMDTTPGGTVLEGNSSSIGAQFKIEVDEGFCSPKPSEIKDFS   900
 901  YVYKPENCQILVGCSMFAPLKTLPSQYLPPIKLPEECIYRQSWTVGKLEL   950
 951  LSSGPSMPFIKEGDGSNMDQEYGTAYTPQTHTSFGMPPSSAPPSNSGAGI  1000
1001  LPSPSTPRFPTPRTPRTPRTPRGAGGPASAQGSVKYENSDLYSPASTPST  1050
1051  CRPLNSVEPATVPSIPEAHSLYVNLILSESVMNLFKDCNFDSCCICVCNM  1100
1101  NIKGADVGVYIPDPTQEAQYRCTCGFSAVMNRKFGNNSGLFLEDELDIIG  1150
1151  RNTDCGKEAEKRFEALRATSAEHVNGGLKESEKLSDDLILLLQDQCTNLF  1200
1201  SPFGAADQDPFPKSGVISNWVRVEERDCCNDCYLALEHGRQFMDNMSGGK  1250
1251  VDEALVKSSCLHPWSKRNDVSMQCSQDILRMLLSLQPVLQDAIQKKRTVR  1300
1301  PWGVQGPLTWQQFHKMAGRGSYGTDESPEPLPIPTFLLGYDYDYLVLSPF  1350
1351  ALPYWERLMLEPYGSQRDIAYVVLCPENEALLNGAKSFFRDLTAIYESCR  1400
1401  LGQHRPVSRLLTDGIMRVGSTASKKLSEKLVAEWFSQAADGNNEAFSKLK  1450
1451  LYAQVCRYDLGPYLASLPLDSSLLSQPNLVAPTSQSLITPPQMTNTGNAN  1500
1501  TPSATLASAASSTMTVTSGVAISTSVATANSTLTTASTSSSSSSNLNSGV  1550
1551  SSNKLPSFPPFGSMNSNAAGSMSTQANTVQSGQLGGQQTSALQTAGISGE  1600
1601  SSSLPTQPHPDVSESTMDRDKVGIPTDGDSHAVTYPPAIVVYIIDPFTYE  1650
1651  NTDESTNSSSVWTLGLLRCFLEMVQTLPPHIKSTVSVQIIPCQYLLQPVK  1700
1701  HEDREIYPQHLKSLAFSAFTQCRRPLPTSTNVKTLTGFGPGLAMETALRS  1750
1751  PDRPECIRLYAPPFILAPVKDKQTELGETFGEAGQKYNVLFVGYCLSHDQ  1800
1801  RWILASCTDLYGELLETCIINIDVPNRARRKKSSARKFGLQKLWEWCLGL  1850
1851  VQMSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCG  1900
1901  ISAADSPSILSACLVAMEPQGSFVIMPDSVSTGSVFGRSTTLNMQTSQLN  1950
1951  TPQDTSCTHILVFPTSASVQVASATYTTENLDLAFNPNNDGADGMGIFDL  2000
2001  LDTGDDLDPDIINILPASPTGSPVHSPGSHYPHGGDAGKGQSTDRLLSTE  2050
2051  PHEEVPNILQQPLALGYFVSTAKAGPLPDWFWSACPQAQYQCPLFLKASL  2100
2101  HLHVPSVQSDELLHSKHSHPLDSNQTSDVLRFVLEQYNALSWLTCDPATQ  2150
2151  DRRSCLPIHFVVLNQLYNFIMNML                            2174

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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