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

NucPred

Fetching Q659K0 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MPLPLPSRSSKPETKKSRSSKIVPSGNNGQSEKRGENYQEKISSSSPRRL    50
  51  CKKRSAFEDLTNASQSQPAQLKKEANKEFVKDVPKKIKGNTPALGLAKSN   100
 101  EVNMVSYKLESSPGVVSTTLVPNITEKPLILERSTTSGTITTEEASFFRK   150
 151  PLILKEESTTEDTGLIKRSLFLKKFTNKGEISLMEKPTSVQEEADSNDEF   200
 201  VVKLITFGKKHKTEEVAITKGTLSLKKMCTYQEDLALQDITVEENSFFME   250
 251  PTNFRKKPKTDDVTPTKKMLSLKKKKYITLGKVSRMKKPLVLQKTNSEDE   300
 301  SPLIKEPLAFKKKPTKKETTFTLRPLSLKKYTTQGKMAHLKKPLESQNTS   350
 351  GEKALIKEPLSFKKKPITKEESLFQEFSASQEKHTTDREVVLLKKPQVLQ   400
 401  EEKDSKDKFLMEPMFLRKKCTTKETNPTKKPLPIKKKCTIQGKMYYLKKP   450
 451  LVLQKTTPGEESFVKEPLSFKKNTTELSMLQEKYTTQEEVSVLKKALTLQ   500
 501  KTLTEEESHLKEPLAFKKKHTTEEATPTKKLSSLKRKRFTAQGKRSCLMK   550
 551  PLVLQTSSGEKTHIKEPLSFKKRSAIEESFFKESPVLQEKHTMQGEVALL   600
 601  EKPGALQENVSSEDEFLMEPISFRKTHTTNEVVSTKEPLSLKKKKCTTQI   650
 651  TMSICQELLDLQNIISKDKASFFMEPVSLREKSLAEEVILTKTPLSLKKK   700
 701  EITQGKIFLLKKPLVSEKTTSEEESLFKKLLPFNKKSTTEGEFLFQDPSV   750
 751  LQEKHTTPQEVSLSTKPLTLPEKTTTEEEPYIKEPLTLEERPTTKEEFLS   800
 801  QEPFSLHAKPTNEDESLFWKALGLQKTQTKEDSLKKLLTLQEKNTTDEES   850
 851  LLNKPSILKEELSTKVATSIEKELSLKKKPTAQGEVFLLKKQLALQENIT   900
 901  NEESLIKQPLAFLKPSIEEAILRESLALQEKPRSEEETLFKEPLSFQEKP   950
 951  TLNEAFHFKEIISLNEKHSTGKELSLKEPLALQENPTQKEDTSLEDSLIL  1000
1001  QVETSSRVPSTPPESRAGMSSVGKLSTTSKSSVCESSSNKPSSSWGESSQ  1050
1051  KEMTPLEDIDRNHGDPFFNSIYAKDIFSYMKEREEKFILKEYMNKQTDIS  1100
1101  SCMRAILVDWLVEVQMTFEMSHETLYLAVKLVDHYLMEVICKRDKLQLLG  1150
1151  STAFLIAAKFEEPCPPCVDDFLYICDDIYQRHEMLSMEISILQTLKFDIN  1200
1201  IPIAYHFLRRYARCLHASMKTLTLSRFICEMTLQEYDYVQERASKLAAGS  1250
1251  FLLALYMMKLRYWVPALEYYSGYKTSDLHPLVKQLNILLTLRPSNKLKTV  1300
1301  YSKYSHQVFFEATKIPPLDMLKLEEILNYC                      1330

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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