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

NucPred

Fetching Q9NJ15 from www.uniprot.org...

The NucPred score for your sequence is 0.69 (see score help below)

   1  MPPAIVILALFTAALCAVNLRTVAADGPRIYRNEWALHVEGGTAAADRLA    50
  51  SKHGFINKGQIGSLEDHYLFVHRRTWKRSLRSSSHRHALLQREPEVRWLQ   100
 101  QQVVKRRVKRRVKRVYSMYPWEQRVQHSSPQVNNPAQQDNLWDPHFNDEK   150
 151  WDKMWYLHCDRPEFACQWSDMNVEAAWKKGYTGKGVVVSILDDGSETDHP   200
 201  DLAGNYDPDASSDINGGTLDPTPRYEYTNENRHGTRCAGEVAAMGNNSFC   250
 251  SVGVAYKASIGGVRMLDGDVTDSVEAASLGLNPQHIMIYSASWGPDDDGK   300
 301  TVDGPANLAQKTFQAGAENGRDKLGSIFVWASGNGGRTHDSCGCDGYTNS   350
 351  IYTISVSSASEQGKVPWYLEPCASTLATTYSSGAPHERKVITTDLRKGCT   400
 401  ESHTGTSASAPMAAGILALALEANPMLTWRDMQYIVVMAANPSPLDRDTE   450
 451  SAYPRDPRKESDFVTNGAGLRVSHNFGFGLMDAGKMVELAESWRRVPEQH   500
 501  VCEEDPNAQQRAITKGETIVDTKTTGGCNGTDHHVKYLEHVVVEISLDHP   550
 551  CRGHLSIHITSPSGTRSTLLPERQFDSSSDGLKDWAFMTTHCWGEQPEGD   600
 601  WILEVKDLGQQNCQRYGLRTVLPVLRKWKLILYGTAEHPLYKRDEESRPH   650
 651  TPQTREEPTDEEECEDGDYYDRSKQRCRHCHDSCATCHGRHSGQCLSCHE   700
 701  GNYFVEDEGTCSEECGQGYYKDEEERKCLDCSADCLTCQVSADHCTSCDD   750
 751  EDGLKLFENTCVAQCSEGRYMDENDVCQDCDDSCDTCTGPDATDCVTCAD   800
 801  EDLLQESQCVESCSSGYFQQEYECLKCHATCASCSGSRDDQCLTCSGHLE   850
 851  LDEDTHRCITSCEDGEYGTEEGKCEDCNIICKKCNGSQADQCLECHHDTN   900
 901  LYDTTCVQYCGNRRYPENGECHPCHPSCLGCIGGEINQCNQCITDYEGED   950
 951  HFLYQGTCHVTCPPGLYGDTTDQVCKACAPGCIACDGPADNQCTLCEEER  1000
1001  APTDGRCQSEGSQTDEAECAEGCHSCEEGPDICDSCDEDYYLTEDTCVRR  1050
1051  TNCPSFTYPDDQDRECRPCHDNCEACDGPNNQNCNSCKEGFYKTPDGCST  1100
1101  GCPNRYYKDDTNKECKPCDSSCFTCSGPASFHCLSCADGDFLHESSCRST  1150
1151  CPAGFIGNAESHECVESSCEQDQYYSSETGRCEDCPYNCRACDNDGDCAE  1200
1201  CAPTYIVVDGRCRPEETCEDGEYQDRDRDTAELSCRPCHQSCKTCSGPSD  1250
1251  TDCDSCKGDDTILDRGECITSCGPGEYMDRREKKCKACHPTCKECSDEYD  1300
1301  DTCTACNDGFLLTDASSCEAGCPPGQFLHHGDCDSCHRECKTCDGPHHDN  1350
1351  CLSCQPGSYLNDQQCSTHCPEGTFEETYEDDSGETVLQCRLCHVNCKTCH  1400
1401  GEGEEDCMECANDIKYKQDGRCVTECQEGHYPDLTNECQQCWSDCETCDG  1450
1451  PRNDQCVTCPYNYYLVLGKCLEDCPEGYYDTMRQEKECGECHPSCATCNE  1500
1501  GGNYNCLSCPYGSKLGEGVCYPMCEEHEYYVEKTQICEECDNSCKTCRGS  1550
1551  TAHDCLSCEAPYGYHAMKHLCTACCEEGSPENEYCCICHESTRLCITDRE  1600
1601  AEGVQFSSADSIPTNVAYIAVATFICVVIVVLFFVVFGMLQARSNGRLCW  1650
1651  AHKYQQVPTTRYEKMNDHVNILSQEDFYNEDSLSEDEIHSIDSTRH      1696

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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