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

NucPred

Fetching Q9ATY5 from www.uniprot.org...

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

   1  MGVQGLWELLAPVGRRVSVETLANKRLAIDASIWMVQFIKAMRDEKGDMV    50
  51  QNAHLIGFFRRICKLLFLRTKPIFVFDGATPALKRRTVIARRRQRENAQT   100
 101  KIRKTAEKLLLNRLKDIRLKEQAKDIKNQRLKQDDSDRVKKRVSSDSVED   150
 151  NLRVPVEEDDVGASFFQEEKLDEVSQASLVGETGVDDVVKESVKDDPKGK   200
 201  GVLLDGDDLDNLVQDSSVQGKDYQEKLDEMLAASLAAEEERNFTSKASTS   250
 251  AAAIPSEEDEEEDSDGDEEILLPVMDGNIDPAVLASLPPSMQLDLLAQMR   300
 301  EKLMAENRQKYQKVKKAPEKFSELQIEAYLKTVAFRREINEVQRSAGGRA   350
 351  VGGVQTSRIASEANREFIFSSSFAGDKEVLASAREGRNDENQKKTSQQSL   400
 401  PVSVKNASPLKKSDATIELDRDEPKNPDENIEVYIDERGRFRIRNRHMGI   450
 451  QMTRDIQRNLHLMKEKERTASGSMAKNDETFSAWENFPTEDQFLEKSPVE   500
 501  KDVVDLEIQNDDSMLHPPSSIEISFDHDGGGKDLNDEDDMFLQLAAGGPV   550
 551  TISSTENDPKEDTSPWASDSDWEEVPVEQNTSVSKLEANLSNQHIPKDIS   600
 601  IAEGVAWEEYSCKNANNSVENDTVTKITKGYLEEEADLQEAIKKSLLELH   650
 651  DKESGDVLEENQSVRVNLVVDKPSEDSLCSRETVGEAEEERFLDEITILK   700
 701  TSGAISEQSNTSVAGNADGQKGITKQFGTHPSSGSNNVSHAVSNKLSKVK   750
 751  SVISPEKALNVASQNRMLSTMAKQHNEEGSESFGGESVKVSAMPIADEEI   800
 801  TGFLDEKDNADGESSIMMDDKRDYSRRKIQSLVTESRDPSRNVVRSRIGI   850
 851  LHDTDSQNERREENNSNEHTFNIDSSTDFEEKGVPVEFSEANIEEEIRVL   900
 901  DQEFVSLGDEQRKLERNAESVSSEMFAECQELLQIFGIPYIIAPMEAEAQ   950
 951  CAFMEQSNLVDGIVTDDSDVFLFGARSVYKNIFDDRKYVETYFMKDIEKE  1000
1001  LGLSRDKIIRMAMLLGSDYTEGISGIGIVNAIEVVTAFPEEDGLQKFREW  1050
1051  VESPDPTILGKTDAKTGSKVKKRGSASVDNKGIISGASTDDTEEIKQIFM  1100
1101  DQHRKVSKNWHIPLTFPSEAVISAYLNPQVDLSTEKFSWGKPDLSVLRKL  1150
1151  CWEKFNWNGKKTDELLLPVLKEYEKRETQLRIEAFYSFNERFAKIRSKRI  1200
1201  NKAVKGIGGGLSSDVADHTLQEGPRKRNKKKVAPHETEDNNTSDKDSPIA  1250
1251  NEKVKNKRKRLEKPSSSRGRGRAQKRGRGRGRVQKDLLELSDGSSDDDDD  1300
1301  DDKVVELEAKPANLQKSTRSRNPVMYSAKEDDELDESRSNEGSPSENFEE  1350
1351  VDEGRIGNDDSVDASINDCPSEDYIQTGGGFCADEADEIGDAHLEDKATD  1400
1401  DYRVIGGGFCVDEDETAEENTMDDDAEILKMESEEQRKKGKRRNEEDASL  1450
1451  DENVDIHFGNSSAGGLSAMPFLKRKKRKN                       1479

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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