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

NucPred

Fetching Q20255 from www.uniprot.org...

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

   1  MDSESDDNPNDPEDRKKWGHKDVEHWRAVSNVHYYAREGYFGTAILVCDG    50
  51  RLATIKDPALAILKGVCLTLLGKIPDAIRHLETFVTDNDVALGALHALKW   100
 101  AHASAFNPDNKSIVEIETEISTRARNEKTPYTSYATASEVLYFAGEYQKS   150
 151  KQMLDIARKRATEKHAKHYCLLGWIELALGKKQKSTQELFEKAGGQEYPD   200
 201  GNIGRCKILEGHHSAPEMKVAANELAISTIHFLPGHIEKAKASIMMKDWR   250
 251  GVMDCIMNADQPEGSNPYIEVLRTVHGICYAGEVSMLKRTLQLLLKSLDE   300
 301  NEATNHVLYARITKLLVSISGRDEKILRHARDFLTRALKISRKPDYVALS   350
 351  MRIAFGLGGAKEVSTLSQELVALDCEDSYAVLSSVVSMLMISRVSDARAQ   400
 401  FDILPSAHPKLLESPLYYLIASVLAKQSKDKSFENFRQHIENLVEMLRNQ   450
 451  LQSFPFGLDYLSLFSSDLLYSAVEQCFDFYPLVPIKAPDDCMKLTAKTLQ   500
 501  MIYDVAPGLAHCTLQLARNSYLCSNTNAAEKWIEKVLDKDDSLADAHILR   550
 551  AELILDRGGKITDADDALVTGLNFNFKLRETSLYHLIKSKTFKKRNENDE   600
 601  AIKTLKMALQIPRKEPSKNLFQPKESADTHKISVQLELIDTLQHMKRIQE   650
 651  AETTMTDALAEWAGQPEQDQLVIAQAQLYLTKGHVERALGILKKIQPGQS   700
 701  NFHLSRIKMAEIYLEEKKDKRMFAACYRELLKVEATPGSYSLLGDAFMKV   750
 751  QEPEDAINFYEQALKMQSKDVQLAEKIGEAYVMAHLYSKAVNFYESSMNI   800
 801  YKDKNMRLKLANLLLKLRNFEKCEKVLRAPFERDPEPVGTETIQTYIQFL   850
 851  LLLAECHEMMDNVPEAMNDFEKAKSLHSRIQDKTLTAALKKEGARICNLQ   900
 901  AELLYRRREFSQAVDICKQALAYHETDLKANLLLSKIFKEENKWTLVLQP   950
 951  CQTVIQVDPHNDEANSILADFYYIRSEAAHASTSYTTLLNTNPQHWHALS  1000
1001  RVVELFCRNGEQNAAEKHLDRAKEVNPRCVTESGYNVCRGRFEWYTGDQN  1050
1051  EALRYYSRTKDSAAGWREKALYYMIDICLNPDNEIIIDENSVENPETTIV  1100
1101  EEASEQQKLAKYYLDLLGKLPTTDRFLLAQNFIRMHTTDKSAIQAALDEF  1150
1151  NRMAFNADRSQVTNVGAVFGVARGHVLLKQVQKAKTVLKMVNGRVWNFDD  1200
1201  SDYLEKCWLMLADIYINQNKNDQAVTFLDLVFKYNCNCLKAFELYGYMRE  1250
1251  KEQKYVEAYKMYEKAFMATKERNPGFGYKLAFTYLKAKRLFACIETCQKV  1300
1301  LDLNPQYPKIKKEIMDKAKALIRT                            1324

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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