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

NucPred

Fetching Q9DE13 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MESGERLTSSSVSSTAAASSPVSSTPSVASAVSKSGLTTGAASLSSTINT    50
  51  GEWWRTADSHSRSGAAFFPPLLGPPLLGISPLFAPPAQNHDSTPFHPRTT   100
 101  GKNNRGSLEKGINGSLNGNSTTAASAISTSVLSTSIATSAGQVKVVTSGA   150
 151  GGRKYNQEQNKVQLLDTRADKIKDKKPRKKAVESSSNSDSDSGSSSDTSS   200
 201  EGISSSDSDDLEEDEEEEEDQSAEESEDDESDSENEAHHENKNKVLMHSG   250
 251  VKDMKTDGQKAHEKSQEKRTHQQIPLVSDSQTHSSFQSQQKQPQVLSQQL   300
 301  PFIFQSSQAKEESVNKHTSVIQSTGLVPNVKPLSLVHQTKKEAYLKIIVP   350
 351  PPDLLKAGNKNTSEESIPLISDVRSKREQYKQTFPAAQLKKQESSKNLKK   400
 401  VIASLSSSKPTSCSPAHQKLTSLENNHSNPFLTNALLGNHQPNGVIQSVI   450
 451  QEVPLALTTKQKSQTKINESVAIASSTPFSLPVNLSACGKKTTGNRTLVV   500
 501  PSTSPVLPGSGKDKPVSNNAVNAVKTQHCLPSAKLVVEQFRGVDSDAPSS   550
 551  KESDDSNDDDDDDEDEDEDDEDDDSDDSQSESDSNSESDTDGSEDEDDED   600
 601  DKDQDESDTDTEGEKTPLKLKKTGSSIKSSSIGPVAHSTPLNLQVAKTPS   650
 651  SAPSALCPETQPAVFLGTTPSTLTPSSHCGISKRRRVTDERELRVPLEYG   700
 701  WQRETRIRNFGGRLQGEVAYFAPCGKKLRQYPEVVKGVQWCLLKEEEVVP   750
 751  CIRAMEGRRGRPPNPDRQHSREESRMRRRKGRPPNVGSTEFLDSTDAKLL   800
 801  RKLQAQEIARQAAQIKLLRKLQKQEQARAAKEAKKQQAIMAAEEKRKQKE   850
 851  QIKIMKQQEKIKRIQQIRMEKELRAQQILEAKKKKKEEAANAKLLEAEKR   900
 901  IKEKEMRRQQAVLLKHQELERHRLDMERERRRQHMMLMKAMEARKKAEEK   950
 951  ERLKQEKRDEKRLNKERKLEQRRLELEMAKELKKPNEDMCLADQKALPEL  1000
1001  PRIPGLVLSGSTFSDCLMIVQFLRNFGKVLGFDVNTDVPSLSTLQEGLLN  1050
1051  IGDSRGEVQDLLVKLVTAAVCDPGLVTGYKAKTILGEHLLNVGINRDNVS  1100
1101  EILQIFMEAHCGQTELTESLKTKAFQAHTPAQKAAVLAFLVNELACSKSV  1150
1151  VSEIDKNIDYMSNLRRDKWMVEGKLRNLRIIHAKKTGKRDATGGGEVGEE  1200
1201  PHSLETPTPGRKRRRKGGDSDYDDDDDDDSDDQADEDDEDEEDKEDKKGK  1250
1251  KAEVCEDEDDGDQTVSVEELEKQIEKLTKQQSQYRKKLFEASHCLRSMMF  1300
1301  GQDRYRRRYWILPQCGGIFVEGMESGEGLEEIAKEKEKLKKVESIHIKEE  1350
1351  VFEISEEKISCLNTTRCEQKEDLKEKDNTNLFLQKPGSFSKLSKLLEVAK  1400
1401  MPPECDVMPQKPNGGAANGCTPSYQNTSQNSLCSLQPSVSQSSSEKSDSS  1450
1451  NLFSPTASGTGKFYSSPLIPSDQLLKTLTEKNRQWFSLLPRVPCDDMSVT  1500
1501  HVDTPATTSLTPQSHPPSKSPSPVPSPLLGSTSAQSPMGLSPFAMPPLQQ  1550
1551  MKPGLPVMGLQFCGWPTGVLTSNVQFSSPLPTLGSGLGLSEGNGNSFLTS  1600
1601  SVPTSKSESPALQTEKVAFATCTAVEVAKPVDHPNPKPIPEEMQYGWWRI  1650
1651  TDPEDLKSLHKVLHLRGIREKALQKQIQKHMDYITLACIKNKDVAIIDIN  1700
1701  ENEDNQVTRDVVENWSVEEQAMEVDLAILQQVEDLERRVASASLQVKGWL  1750
1751  CPEPASEREDLVYHEHKSIIRLHKKHDGDSAGGGEGSTSSLERKNDNPLD  1800
1801  IAVTRLADLERNIERRYLKSPLSTTIQIKLDNVGTVTVPAPAPSISGDGD  1850
1851  GTEEDIAPGLRVWRKALSEARSAAQVALCIQQLQKSIAWEKSIMKVYCQI  1900
1901  CRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPDGDWFCPACIAKASGQT  1950
1951  LKLKKLQIKGKKSNEQKRGRKLPGDTEDEDSATTSTSLKRGKTEPKKRKM  2000
2001  DESVSVSQGKQENFTAIKKPKRDDSKDLAICSMILSELETHEDAWPFLLP  2050
2051  VNLKLVPGYKKVIKKPMDFSTIRDKLTSGQYPNVEAFSLDVRLVFDNCET  2100
2101  FNEDDSDIGRAGHNMRKYFEKKWTEIFKLS                      2130

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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