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

NucPred

Fetching P34369 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MANYGGHPQTEPHAIPDSILEEKSRKWKQLQGKRYSEKKKFGMSDTQKEE    50
  51  MPPEHVRKVIRDHGDMTSRKYRHDKRVYLGALKYMPHAVLKLLENMPMPW   100
 101  EQIRDVKVLYHITGAITFVNDIPRVIEPVYMAQWGTMWIMMRREKRDRRH   150
 151  FKRMRFPPFDDEEPPLDYADNILDVEPLEPIQMELDPEEDGAVAEWFYDH   200
 201  KPLATTRFVNGPTYRKWAFSIPQMSTLYRLANQLLTDLVDDNYFYLFDMK   250
 251  SFFTAKALNVAIPGGPKFEPLVKDLHTDEDWNEFNDINKVIIRAPIRTEY   300
 301  RIAFPFMYNNLISSLPVQVSWYHTPSVVFIKTEDPDLPAFYYDPLINPIV   350
 351  LSNLKATEENLPEGEEEDEWELPEDVRPIFEDVPLYTDNTANGLALLWAP   400
 401  RPFNLRSGRTRRAVDVPLVKSWYREHCPAGMPVKVRVSYQKLLKVFVLNA   450
 451  LKHRPPKPQKRRYLFRSFKATKFFQTTTLDWVEAGLQVLRQGYNMLNLLI   500
 501  HRKNLNYLHLDYNFNLKPVKTLTTKERKKSRFGNAFHLCREILRLTKLVV   550
 551  DAHVQYRLNNVDAYQLADGLQYIFAHVGQLTGMYRYKYKLMRQVRMCKDL   600
 601  KHLIYYRFNTGPVGKGPGCGFWAPGWRVWLFFLRGITPLLERWLGNLLSR   650
 651  QFEGRHSKGVAKTVTKQRVESHFDLELRAAVMHDILDMMPDGIKQNKARV   700
 701  ILQHLSEAWRCWKANIPWKVPGLPTPVENMILRYVKAKADWWTNSAHYNR   750
 751  ERVRRGATVDKTVCKKNLGRLTRLYLKSEQERQHNYLKDGPYISAEEAVA   800
 801  IYTTTVHWLESRRFSPIPFPPLSYKHDTKLLILALERLKESYSVKNRLNQ   850
 851  SQREELALIEQAYDNPHEALSRIKRHMLTQRAFKEVGIEFMDLYTHLIPV   900
 901  YDIEPLEKVTDAYLDQYLWYEADKRRLFPAWVKPGDTEPPPLLTYKWCQG   950
 951  LNNLQDVWETSEGECNVIMETKLEKIAEKMDLTLLNRLLRLIVDHNIADY  1000
1001  MTSKNNVLINYKDMNHTNSFGIIRGLQFASFIVQFYGLVLDLLVLGLRRA  1050
1051  SEIAGPPQCPNEFLQFQDVATEIGHPIRLYCRYIDRVWIMFRFSADEARD  1100
1101  LIQRYLTEHPDPNNENIVGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIK  1150
1151  NRLPRSITTVEWENSFVSVYSKDNPNMLFDMSGFECRILPKCRTANEEFV  1200
1201  HRDGVWNLQNEVTKERTAQCFLKVDEESLSKFHNRIRQILMSSGSTTFTK  1250
1251  IVNKWNTALIGLMTYFREAVVNTQELLDLLVKCENKIQTRIKIGLNSKMP  1300
1301  SRFPPVVFYTPKEIGGLGMLSMGHVLIPQSDLRWMQQTEAGGVTHFRSGM  1350
1351  SHDEDQLIPNLYRYIQPWEAEFVDSVRVWAEYALKRQEANAQNRRLTLED  1400
1401  LDDSWDRGIPRINTLFQKDRHTLAYDKGWRVRTEFKAYQILKQNPFWWTH  1450
1451  QRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFRGTYFPTWEGLFWERAS  1500
1501  GFEESMKFKKLTNAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDL  1550
1551  TGIFMHGKIPTLKISLIQIFRAHLWQKIHESVVMDLCQVFDQELDALEIQ  1600
1601  TVQKETIHPRKSYKMNSSCADVLLFAQYKWNVSRPSLMADSKDVMDNTTT  1650
1651  QKYWLDVQLRWGDYDSHDVERYARAKFLDYTTDNMSIYPSPTGVLIAIDL  1700
1701  AYNLYSAYGNWFPGMKPLIRQAMAKIIKANPAFYVLRERIRKGLQLYSSE  1750
1751  PTEPYLTSQNYGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAI  1800
1801  FIFNPRTGQLFLKIIHTSVWAGQKRLSQLAKWKTAEEVAALIRSLPVEEQ  1850
1851  PRQIIVTRKAMLDPLEVHLLDFPNIVIKGSELMLPFQAIMKVEKFGDLIL  1900
1901  KATEPQMVLFNLYDDWLKTISSYTAFSRVVLIMRGMHINPDKTKVILKPD  1950
1951  KTTITEPHHIWPTLSDDDWIKVELALKDMILADYGKKNNVNVASLTQSEV  2000
2001  RDIILGMEISAPSQQRQQIADIEKQTKEQSQVTATTTRTVNKHGDEIITA  2050
2051  TTSNYETASFASRTEWRVRAISSTNLHLRTQHIYVNSDDVKDTGYTYILP  2100
2101  KNILKKFITISDLRTQIAGFMYGVSPPDNPQVKEIRCIVLVPQTGSHQQV  2150
2151  NLPTQLPDHELLRDFEPLGWMHTQPNELPQLSPQDVTTHAKLLTDNISWD  2200
2201  GEKTVMITCSFTPGSVSLTAYKLTPSGYEWGKANTDKGNNPKGYMPTHYE  2250
2251  KVQMLLSDRFLGYFMVPSNGVWNYNFQGQRWSPAMKFDVCLSNPKEYYHE  2300
2301  DHRPVHFHNFKAFDDPLGTGSADREDAFA                       2329

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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