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

NucPred

Fetching Q9C8Z4 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MSSSIVSQLQALKSVLQADTEPSKRPFTRPSILFSPKEAADFDIESIYEL    50
  51  GLKGLEVLGNKDERFKNYMNDLFSHKSKEIDRELLGKEENARIDSSISSY   100
 101  LRLLSGYLQFRASLETLEYLIRRYKIHIYNLEDVVLCALPYHDTHAFVRI   150
 151  VQLLSTGNSKWKFLDGVKNSGAPPPRSVIVQQCIRDKQVLEALCDYASRT   200
 201  KKYQPSKPVVSFSTAVVVGVLGSVPTVDGDIVKTILPFVDSGLQSGVKGC   250
 251  LDQQAGALMVVGMLANRAVLNTNLIKRLMRSIIDIGREHAKESSDPHSLR   300
 301  LSLMALINFVQLQSVDLIPRKALDLFNEIRDISGVLLGLSKEFNIKRFLA   350
 351  VLLDSLLFYSSSDDKCCEVLASIIETVPVSNLVDHLISKVFSLCMTQYQK   400
 401  NSDFRSSTSGSWAKKFLVVVSKKYPAELRAAVPKFLEATEVQSKKEDLKL   450
 451  EMLSCMLDGNSDMSHPFVDSKLWFRLHHPRAAVRCAALSSLNGVLKDDSS   500
 501  KAENLVTIQDAILRQLWDDDLAVVQAALSFDKLPNIITSSGLLDALLHVV   550
 551  KRCVGILVSGVSHNVQLAVDVVALSLKIAVSSFGNQTDSTEKVTSAMFPF   600
 601  LLIQPKTWNLNLLVLKLGKDVNWPLFKNLAADDGMKKLPDIMSTNLSSIS   650
 651  MDIINDLGEALSLDPDERRIELIERACNYKLSEVLETCSNIKCSEQDRNK   700
 701  LQKGLLIRESVSALNIDVINKLVEAFMMHPADYIQWLTVSCRDSTLSKTL   750
 751  FYMILMHSLQKMNSSSDPSQLLDLFELCFPVLKTEWEELEVEVDVSLKEL   800
 801  SKSNCQELLYQLLDTSDFTALNSKVLICLFWKLGESFIKLEPAHDASVLN   850
 851  KRLSSGLEDLFFFFATTRLRHVFKEHLHFRVREAKVCPVLFLSRLISRED   900
 901  VPPLVQIESLRCFSYLCSSGNNEWLIQVFSSFPVLLVPMSSDNQDVKAAA   950
 951  INCIEALFNLRAAIYGSSFDELLGMIVQQRRLILSDNKFFASYLTSLLSS  1000
1001  TTNDLLVPVGLQKRFDQSTKENILSVILLCAEDLPAYGKLRVLSLLKDLG  1050
1051  IMLMRDEIVKLLSQLLDKRSQYYYKLDKTSQPLSDTEVDLLCLLLECSMM  1100
1101  RTSSFKGQSLDDHILSALNVDCMASERPAVISPCLTILEKLSNRFYDELQ  1150
1151  TDVQIRFFHKLVSMFRSSNGSIQNGAKEAVLRLKLSSSTVVLALDRITQQ  1200
1201  DTLVIGSLSKKKKQKKNSKSCPEEDINSEEFRSGEKALSFIASLLDMLLL  1250
1251  KKDLTHRESLIRPLFKLLQRSMSKEWVKIAFSIEETSLQPPQDVRETTPT  1300
1301  FISSIQQTLLLILKDIFDSLNMNPLKAEVANEINVKMLVELAHSSNDGVT  1350
1351  RNHIFSLFTAIVKFVPDKVLDHIISILTLVGESTVTQIDSHSKSIFEGFI  1400
1401  SMVIPFWLSKTKSEEQLLQIFVKVLPDIVEHRRRSIVAYLLGVIGERNGL  1450
1451  PALLVLLFKSLISRKDSAWLGNANVSESFASIVKKEWEYSFAMEICEQYS  1500
1501  SSTWLSSLVILLQTISKDSKQCFLQMRLVLEFVFQKLQDPEFAFAVSLEP  1550
1551  RNNVSVGIQQELQELMKCCICLLQAIDAKKEKDVTSSVRNEIRMRIHDVL  1600
1601  MTVTGAMDLSIYFRVVTSLLQQQTDYNGTKKVLGLISERAKDTSSSKMKH  1650
1651  KRKISNQKGRNSWLNLDEVAVDSFGKMCEEIVHLINATDDESGVPVKRAA  1700
1701  ISTLEVLAGRFPSGHPIFRKCLAAVAECISSKNLGVSSSCLRTTGALINV  1750
1751  LGPKALIELPCIMKNLVKQSLEVSFASQSGRNATAEEQLLMLSVLVTLEA  1800
1801  VIDKLGGFLNPHLGDIMKIMVLHPEYVSDFDKNLKSKANAIRRLLTDKIP  1850
1851  VRLTLQPLLRIYNEAVSSGNASLVIAFNMLEDLVVKMDRSSIVSSHGKIF  1900
1901  DQCLVALDIRRLNPAAIQNIDDAERSVTSAMVALTKKLTESEFRPLFIRS  1950
1951  IDWAESDVVDGSGSENKSIDRAISFYGLVDRLCESHRSIFVPYFKYVLDG  2000
2001  IVAHLTTAEASVSTRKKKKAKIQQTSDSIQPKSWHLRALVLSCLKNCFLH  2050
2051  DTGSLKFLDTNNFQVLLKPIVSQLVVEPPSSLKEHPHVPSVDEVDDLLVS  2100
2101  CIGQMAVASGSDLLWKPLNHEVLMQTRSESVRSRMLSLRSVKQMLDNLKE  2150
2151  EYLVLLAETIPFLAELLEDVELSVKSLAQDIIKQMEEMSGESLAEYL     2197

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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