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

NucPred

Fetching P31695 from www.uniprot.org...

The NucPred score for your sequence is 0.63 (see score help below)

   1  MQPQLLLLLLLPLNFPVILTRELLCGGSPEPCANGGTCLRLSRGQGICQC    50
  51  APGFLGETCQFPDPCRDTQLCKNGGSCQALLPTPPSSRSPTSPLTPHFSC   100
 101  TCPSGFTGDRCQTHLEELCPPSFCSNGGHCYVQASGRPQCSCEPGWTGEQ   150
 151  CQLRDFCSANPCANGGVCLATYPQIQCRCPPGFEGHTCERDINECFLEPG   200
 201  PCPQGTSCHNTLGSYQCLCPVGQEGPQCKLRKGACPPGSCLNGGTCQLVP   250
 251  EGHSTFHLCLCPPGFTGLDCEMNPDDCVRHQCQNGATCLDGLDTYTCLCP   300
 301  KTWKGWDCSEDIDECEARGPPRCRNGGTCQNTAGSFHCVCVSGWGGAGCE   350
 351  ENLDDCAAATCAPGSTCIDRVGSFSCLCPPGRTGLLCHLEDMCLSQPCHV   400
 401  NAQCSTNPLTGSTLCICQPGYSGSTCHQDLDECQMAQQGPSPCEHGGSCI   450
 451  NTPGSFNCLCLPGYTGSRCEADHNECLSQPCHPGSTCLDLLATFHCLCPP   500
 501  GLEGRLCEVEVNECTSNPCLNQAACHDLLNGFQCLCLPGFTGARCEKDMD   550
 551  ECSSTPCANGGRCRDQPGAFYCECLPGFEGPHCEKEVDECLSDPCPVGAS   600
 601  CLDLPGAFFCLCRPGFTGQLCEVPLCTPNMCQPGQQCQGQEHRAPCLCPD   650
 651  GSPGCVPAEDNCPCHHGHCQRSLCVCDEGWTGPECETELGGCISTPCAHG   700
 701  GTCHPQPSGYNCTCPAGYMGLTCSEEVTACHSGPCLNGGSCSIRPEGYSC   750
 751  TCLPSHTGRHCQTAVDHCVSASCLNGGTCVNKPGTFFCLCATGFQGLHCE   800
 801  EKTNPSCADSPCRNKATCQDTPRGARCLCSPGYTGSSCQTLIDLCARKPC   850
 851  PHTARCLQSGPSFQCLCLQGWTGALCDFPLSCQKAAMSQGIEISGLCQNG   900
 901  GLCIDTGSSYFCRCPPGFQGKLCQDNVNPCEPNPCHHGSTCVPQPSGYVC   950
 951  QCAPGYEGQNCSKVLDACQSQPCHNHGTCTSRPGGFHCACPPGFVGLRCE  1000
1001  GDVDECLDRPCHPSGTAACHSLANAFYCQCLPGHTGQRCEVEMDLCQSQP  1050
1051  CSNGGSCEITTGPPPGFTCHCPKGFEGPTCSHKALSCGIHHCHNGGLCLP  1100
1101  SPKPGSPPLCACLSGFGGPDCLTPPAPPGCGPPSPCLHNGTCTETPGLGN  1150
1151  PGFQCTCPPDSPGPRCQRPGASGCEGRGGDGTCDAGCSGPGGDWDGGDCS  1200
1201  LGVPDPWKGCPPHSQCWLLFRDGRCHPQCDSEECLFDGYDCEIPLTCIPA  1250
1251  YDQYCRDHFHNGHCEKGCNNAECGWDGGDCRPEGEDSEGRPSLALLVVLR  1300
1301  PPALDQQLLALARVLSLTLRVGLWVRKDSEGRNMVFPYPGTRAKEELSGA  1350
1351  RDSSSWERQAPPTQPLGKETESLGAGFVVVMGVDLSRCGPEHPASRCPWD  1400
1401  SGLLLRFLAAMAAVGALEPLLPGPLLAAHPQAGTRPSANQLPWPILCSPV  1450
1451  VGVLLLALGALLVLQLIRRRRREHGALWLPPGFIRRPQTQQAPHRRRPPL  1500
1501  GEDNIGLKALKPEAEVDEDGVAMCSGPEEGEAEETASASRCQLWPLNSGC  1550
1551  GELPQAAMLTPPQECESEVLDVDTCGPDGVTPLMSAVFCGGVQSTTGASP  1600
1601  QRLGLGNLEPWEPLLDRGACPQAHTVGTGETPLHLAARFSRPTAARRLLE  1650
1651  AGANPNQPDRAGRTPLHTAVAADAREVCQLLLASRQTTVDARTEDGTTPL  1700
1701  MLAARLAVEDLVEELIAARADVGARDKRGKTALHWAAAVNNARAARSLLQ  1750
1751  AGADKDAQDSREQTPLFLAAREGAVEVAQLLLELGAARGLRDQAGLAPGD  1800
1801  VARQRSHWDLLTLLEGAGPTTQEARAHARTTPGGGAAPRCRTLSAGARPR  1850
1851  GGGACLQARTWSVDLGARGGKVYARCRSRSGSCGGPTTRGRRFSAGSRGR  1900
1901  RGARASQDDWPRDWVALEACGSACSAPIPPPSLTPSPERGSPQVAWGLPV  1950
1951  HQEIPLNSVVRNLN                                      1964

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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