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

NucPred

Fetching Q9QW30 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MPALRPAALRALLWLWLCGAGPAHALQCRGGQEPCVNEGTCVTYHNGTGY    50
  51  CRCPEGFLGEYCQHRDPCEKNRCQNGGTCVTQAMLGKATCRCAPGFTGED   100
 101  CQYSTSHPCFVSRPCQNGGTCHMLSWDTYECTCQVGFTGKQCQWTDVCLS   150
 151  HPCENGSTCSSVANQFSCRCPAGITGQKCDADINECDIPGRCQHGGTCLN   200
 201  LPGSYRCQCPQRFTGQHCDSPYVPCAPSPCVNGGTCRQTGDFTSECHCLP   250
 251  GFEGSNCERNIDDCPNHKCQNGGVCVDGVNTYNCRCPPQWTGQFCTEDVD   300
 301  ECLLQPNACQNGGTCTNRNGGYGCVCVNGWSGDDCSENIDDCAFASCTPG   350
 351  STCIDRVASFSCLCPEGKAGLLCHLDDACISNPCHKGALCDTNPLNGQYI   400
 401  CTCPQAYKGADCTEDVDECAMANSNPCEHAGKCVNTDGAFHCECLKGYAG   450
 451  PRCEMDINECHSDPCQNDATCLDKIGGFTCLCMPGFKGVHCELEVNECQS   500
 501  NPCVNNGQCVDKVNRFQCLCPPGFTGPVCQIDIDDCSSTPCLNGAKCIDH   550
 551  PNGYECQCATGFTGTLCDENIDNCDPDPCHHGQCQDGIDSYTCICNPGYM   600
 601  GAICSDQIDECYSSPCLNDGRCIDLVNGYQCNCQPGTSGLNCEINFDDCA   650
 651  SNPCLHGACVDGINRYSCVCSPGFTGQRCNIDIDECASNPCRKDATCIND   700
 701  VNGFRCMCPEGPHHPSCYSQVNECLSSPCIHGNCTGGLSGYKCLCDAGWV   750
 751  GINCEVDKNECLSNPCQNGGTCNNLVNGYRCTCKKGFKGYNCQVNIDECA   800
 801  SNPCLNQGTCLDDVSGYTCHCMLPYTGKNCQTVLAPCSPNPCENAAVCKE   850
 851  APNFESFTCLCAPGWQGQRCTVDVDECVSKPCMNNGICHNTQGSYMCECP   900
 901  PGFSGMDCEEDINDCLANPCQNGGSCVDKVNTFSCLCLPGFVGDKCQTDM   950
 951  NECLSEPCKNGGTCSDYVNSYTCTCPAGFHGVHCENNIDECTESSCFNGG  1000
1001  TCVDGINSFSCLCPVGFTGPFCLHDINECSSNPCLNSGTCVDGLGTYRCT  1050
1051  CPLGYTGKNCQTLVNLCSPSPCKNKGTCAQEKARPRCLCPPGWDGAYCDV  1100
1101  LNVSCKAAALQKGVPVEHLCQHSGICINAGNTHHCQCPLGYTGSYCEEQL  1150
1151  DECASNPCQHGATCSDFIGGYRCECVPGYQGVNCEYEVDECQNQPCQNGG  1200
1201  TCIDLVNHFKCSCPPGTRGLLCEENIDDCAGAPHCLNGGQCVDRIGGYSC  1250
1251  RCLPGFAGERCEGDINECLSNPCSSEGSLDCIQLKNNYQCVCRSAFTGRH  1300
1301  CETFLDVCPQKPCLNGGTCAVASNVPDGFICRCPPGFSGARCQSSCGQVK  1350
1351  CRRGEQCVHTASGPHCFCPNHKDCESGCASNPCQHGGTCYPQRQPPYYSC  1400
1401  RCSPPFWGSHCESYTAPTSTPPATCLSQYCADKARDGICDEACNSHACQW  1450
1451  DGGDCSLTMEDPWANCTSSLRCWEYINNQCDELCNTAECLFDNFECQRNS  1500
1501  KTCKYDKYCADHFKDNHCDKGCNNEECGWDGLDCAADQPENLAEGILVIV  1550
1551  VLLPPEQLLQDSRSFLRALGTLLHTNLRIKQDSQGALMVYPYYGEKSAAM  1600
1601  KKQKVARRSLPDEQEQEIIGSKVFLEIDNRQCVQDSDQCFKNTDAAAALL  1650
1651  ASHAIQGTLSYPLVSVVSESEDPRNTPLLYLLAVAVVIILFLILLGVIMA  1700
1701  KRKRKHGFLWLPEGFTLRRDSSNHKRREPVGQDAVGLKNLSVQVSEANLI  1750
1751  GSTTSEHWGDDEGPQPKKAKAEDDEALLSEDDPVDRRPWTQQHLEAADIR  1800
1801  RTPSLALTPPQAEQEVDVLDVNVRGPDGCTPLMLASLRGGSSDLSDEDED  1850
1851  AEDSSANIITDLVYQGASLQAQTDRTGEMALHLAARYSRADAAKRLLDAG  1900
1901  ADANAQDNMGRCPLHAAVAADAQGVFQILIRNRVTDLDARMNDGTTPLIL  1950
1951  AARLAVEGMVAELINCQADVNAVDDHGKSALHWAAAVNNVEATLLLLKNG  2000
2001  ANRDMQDNKEETPLFLAAREGSYEAAKILLDHFANRDITDHMDRLPRDVA  2050
2051  RDRMHHDIVRLLDEYNVTPSPPGTVLTSALSPVLCGPNRSFLSLKHTPMG  2100
2101  KKARRPNTKSTMPTSLPNLAKEAKDVKGSRRKKCLNEKVQLSESSVTLSP  2150
2151  VDSLESPHTYVSDATSSPMITSPGILQASPTPLLAAAPAAPVHAQHALSF  2200
2201  SNLHEMQPLRPGASTVLPSVSQLLSHHHIVPPGSGSAGSLGRLHSVPVPS  2250
2251  DWMNRVEMSETQYSEMFGMVLAPAEGTHPGMAAPQSRAPEGKPIPTQREP  2300
2301  LPPIVTFQLIPKGSLAQAAGAPQTQSGCPPAVAGPLPSMYQIPEMARLPS  2350
2351  VAFPPTMMPQQEGQVAQTIVPTYHPFPASVGKYPTPPSQHSYASSNAAER  2400
2401  TPNHGGHLQGEHPYLTPSPESPDQWSSSSPHSASDWSDVTTSPTPGGGGG  2450
2451  GQRGPGTHMSEPPHSNMQVYA                               2471

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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