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

NucPred

Fetching Q9GLP1 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MFPALPCPWVLVVLGTSWAAWGNLGTEAARVRQFYVAAQSISWNYHPEPT    50
  51  HPSSSPFATSFKKIVYREYEAYFQKEKPPSRMSGLLGPTLYADVGDIMKV   100
 101  HFRNKADKPLSIHPQGIKYSKFAEGASYPDHTFLVEKMDDAVAPGQEYTY   150
 151  EWNISEDSGPTHNDPPCLTHIYYSYENLIQDFNSGLIGPLLICKKGTLTE   200
 201  DGIQKMFDKQYVLMFAVFDESKSWNQSSSLMYTVNGYVNGTMPDITVCAY   250
 251  DHISWHLIGMSSGPELFSIHFSGQVLEQNHHKVSAITLVSATSTTANMTV   300
 301  SPEGKWPISSLIPKHFQAGMQAYIDIKNCAKKTRKPKKLTRDQRRHIKRW   350
 351  EYFIAAEEVIWDYAPIIPANMDKKYRSLHLDNFSNQIGKHYKKVVYKQYQ   400
 401  DESFTKRLENPNNKEDGILGPVIRAQVRDTLKIVFKNMASRSYSIYPHGV   450
 451  TFSPYEDDVNSSSTSDNNTMIRAVQPGETYTYKWNILESDEPTENDAQCL   500
 501  TRPYYSNVDITRDIASGLIGLLLICKSRSLDKRGIQRTADIEQKAVFAVF   550
 551  DENKSWYIEDNIYKFCENPEKVKRDDPKFYESNIMSTINGYVPESIPTLG   600
 601  FCFDDTVQWHFCSVRTHDNILTIHFTGHSFIYGKRHEDTLTLFPMRGESV   650
 651  TVTMDNVGTWMLTTMNSNPRNKKLQLKFRDVKCIRDDDEDSYEIIYEPSS   700
 701  STTLTTRKMHDSSENKEEENDDEYDYQDLLASVLGIRSFRNSSLYQEDDE   750
 751  FNLTALALENNSEFIPPSTDRAVDSNSSSPGNISRAPANTFTEPRKILPH   800
 801  PEATKAGSPRRHTGLVKNLVLNRRRTQHSDPYSEDPIENPLQSVITGISL   850
 851  LPFGTEGFRNREHPKHKRFKAGRDQAAKHRFSQMEFPAHKTGRHISQDNS   900
 901  SSSSMGPLEDLSSDLLLLERKDPSTINGKWHLVSEKGSYEIVQDADEDMA   950
 951  VNKLPNNPQNASRSWGENIPFTNKHGKQRGHPIFVTRHKLLQERQDEGNS  1000
1001  ILKKGRFFIRTRRKKKERKPVHHVPLSPRSFNPLRGEANTPFSDRRQNHS  1050
1051  LLLHESNETFPPTDLNQTFPSMNLSLIASHPDHNQNLPNDTHQTSSPLDL  1100
1101  YQTVTPDEPYQTAPIQDLDPTHSTAVPSHQSSLPEPIQMHDYDLRNKASP  1150
1151  TDVSEMFFSLKLKAGHRTTSPDLNQTSLSPELSQTTLSPDPGHVTLSPDL  1200
1201  SQTTLSPDLSHTTLSPDLGHTTLSPDLSHTTLSPDLSQTTLSPDLSHTTL  1250
1251  SPDLGHTTLSPDLSHTTLSPDLGHATLSPDLSHTTLSPDLGHTTLSPDLG  1300
1301  HTTLSPDFSQTTLSPDLGHTTLSSDVSHTTLSPDLSHTTLSPDLSHTTLS  1350
1351  PDLGHTTLSPDLSQTTLSPDLGHMTLSPDLSHTTLSPDLGHTTLSPDLSH  1400
1401  TTLSPDLGHMTLSPDLGQTTLSLDFGQTTLSPDLSHMTLSSELSHETLSP  1450
1451  DLSQVTLSPDLSEIPFSPDLWQTTLSSDLNETTLSPDLRQTSPHPDPDKT  1500
1501  SYISESSQSVTLPEFGQTSPFPDLGQRPSPPSHSTLNNTFIPREFNPMVV  1550
1551  VGLSRDDGDYVEIIPRQQEENSEEDYVKIDYVEYDDPYQTDVRTDINSSR  1600
1601  NPDNIAAWYLRSNNGNRRNYYIAAEELSWDYSKFTQREDIDDVPEHTIYK  1650
1651  KVVFRKYLDSTFTKLDPRGEYEEHLGILGPIIRAEVDDVIQVRFKNLASR  1700
1701  PYSLHAHGLSYEKSSEGKTYEDDSPEWFKEDNAVQPNSSYTYVWHATERS  1750
1751  GPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICRKGTLHKENNMPVDM  1800
1801  REFVLLFMVFDEKKSWYYEKKFTRSWRLTSSEVKNSHKFHAINGMIYNLP  1850
1851  GLRMYEQEWVRLHLLNLGGSRDIHVVHFHGQTLLENGTQQHQLGVWPLLP  1900
1901  GSFKTLEMKTSKAGWWLLDTEVGENQRAGMQTPFLIIDRECKMPMGLSTG  1950
1951  LIADSQIKASEFWGHWQPKLARLNNGGSYNAWITDKFSGESNSKPWIQVD  2000
2001  MQREVVFTGIQTQGAKYYLKSYYTTEFNVAYSSDQRNWRIFKGNSTKNVM  2050
2051  YFNGNSDASTITENQFDPPVVARYIRISPTESYNKPALRLELQGCEVNGC  2100
2101  STPLGMESGNIKNEQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKA  2150
2151  NNNNQWLQIDLLKIKKITAITTQGCKSLSSEMYVKRYTIQYSDRGVEWKS  2200
2201  YREKSSMVDKIFEGNNNIKGHVKNFFNPPIISRFIRIIPKMWNQSIALRL  2250
2251  ELFGCDIY                                            2258

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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