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

NucPred

Fetching Q6ZPZ3 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MEAVPGTPPPPPSESPPPPSPPPPSTPSPPPCSPDGRAATPHLLHHRLPL    50
  51  PDDREDGELEEGELEDDGAEEVQDPPGGQERSRKEKGEKHHSDSEEEKSH   100
 101  RRLKRKRKKEREKEKRRSKKRRKSKHKRHASSSDDFSDFSDDSDFSPSEK   150
 151  SHRKYRDYSPPYAPSHQQYSSSHNAPLPKKSYSKMDSKGYSMYEDYENEQ   200
 201  YGEYEGDEEEDMGKEDYDDFTKELNQYRRAKEGSSRGRGSRGRGRGYRGR   250
 251  GSRGGSRGRGMGRGSRGRGRGSMGEHPEDEEDLYEEEIEYGESEEPMGDD   300
 301  DYDDYSKELNQYRRSKDSRGRGLSRGRGRGSRGGRGKGMGRGRGRGGRGG   350
 351  MSKGGMNDDEDFYDDDMGDGGGGSYRRSDHDKPHQQSDKKGKVICKYFVE   400
 401  GRCTWGDHCNFSHDIELPKKRELCKFYITGFCARAENCPYMHGDFPCKLY   450
 451  HTTGNCINGDDCMFSHDPLTEETRELLDKMLADDAEAGAEDEKEVEELKK   500
 501  QGINPLPKPPPGVGLLPTPPRPPGPPAPTSPNGRPMQGGPPPPPPPPPPP   550
 551  PGPPQMSLPTHEPLSPQQLQQDMYNKKIPSLFEIVVRPTGQLAEKLGVRF   600
 601  PGPGGPSGPMGPGPNMGPPGPMGGPMHPDMHPDMHPDMHPDMHPDMHPDM   650
 651  HPDMHPDMHPDMPMGPGMNPGPPMGPGGPPMMPYGPGDSPHSGMMPPIPP   700
 701  AQNFYENFYPQQEGMEMEPGLVGDAEDYGHYEELPGQPGEPLFPEHPLEP   750
 751  DSFPEGGPPGRPKAGAGVPDFLPSAQRALYLRIQQKQQEEERARRLAESS   800
 801  KQDRENEEGDTGNWYSSDEDEGGSSVTSILKTLRQQTSSRPQASVGEPSS   850
 851  SGLGDPRLQKGHPTGSRLSDPRLSRDPRLSRHAETSGGSGPGDSGPSDPR   900
 901  LARALPTSKAEGSLHSSPAGPSSSKGQPPAEEEEGERALREKAVNIPLDP   950
 951  LPGHPLRDPRSQLQQFSHIKKDVTLSKPSFARTVLWNPEDLIPLPIPKQD  1000
1001  VPPVPAALQSLPALDPRLHRSTPPGPPNTRQRPGSTDPSTSGSNLPDFEL  1050
1051  LSRILKTVNVNTPGQSEKPSDPRVRKTPTDPRLQKPADPVAASRAAKPCP  1100
1101  TEASPPAASPSGDSSPPATAPYDPRVLAAGGLGQGSSSGQSSVLSGISLY  1150
1151  DPRTPNAGGKTAEPASDTSAQPKGPEGNGKGSASKAKEPPFVRKSALEQP  1200
1201  ETGKASTDGATATDRYNSYNRPRPKATAAPTAASSTPPPEGATPQPGVHN  1250
1251  LPVPTLFGTVKPAPKTGTGSPFAGNSPAREGEQDAGSLKDVFKGFDPTAS  1300
1301  PFCQ                                                1304

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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