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

NucPred

Fetching Q9NRD8 from www.uniprot.org...

The NucPred score for your sequence is 0.52 (see score help below)

   1  MLRARPEALMLLGALLTGSLGPSGNQDALSLPWEVQRYDGWFNNLRHHER    50
  51  GAVGCRLQRRVPANYADGVYQALEEPQLPNPRRLSNAATRGIAGLPSLHN   100
 101  RTVLGVFFGYHVLSDVVSVETPGCPAEFLNIRIPPGDPVFDPDQRGDVVL   150
 151  PFQRSRWDPETGRSPSNPRDLANQVTGWLDGSAIYGSSHSWSDALRSFSG   200
 201  GQLASGPDPAFPRDSQNPLLMWAAPDPATGQNGPRGLYAFGAERGNREPF   250
 251  LQALGLLWFRYHNLWAQRLARQHPDWEDEELFQHARKRVIATYQNIAVYE   300
 301  WLPSFLQKTLPEYTGYRPFLDPSISPEFVVASEQFFSTMVPPGVYMRNAS   350
 351  CHFRKVLNKGFQSSQALRVCNNYWIRENPNLNSTQEVNELLLGMASQISE   400
 401  LEDNIVVEDLRDYWPGPGKFSRTDYVASSIQRGRDMGLPSYSQALLAFGL   450
 451  DIPRNWSDLNPNVDPQVLEATAALYNQDLSQLELLLGGLLESHGDPGPLF   500
 501  SAIVLDQFVRLRDGDRYWFENTRNGLFSKKEIEDIRNTTLRDVLVAVINI   550
 551  DPSALQPNVFVWHKGAPCPQPKQLTTDGLPQCAPLTVLDFFEGSSPGFAI   600
 601  TIIALCCLPLVSLLLSGVVAYFRGREHKKLQKKLKESVKKEAAKDGVPAM   650
 651  EWPGPKERSSPIIIQLLSDRCLQVLNRHLTVLRVVQLQPLQQVNLILSNN   700
 701  RGCRTLLLKIPKEYDLVLLFSSEEERGAFVQQLWDFCVRWALGLHVAEMS   750
 751  EKELFRKAVTKQQRERILEIFFRHLFAQVLDINQADAGTLPLDSSQKVRE   800
 801  ALTCELSRAEFAESLGLKPQDMFVESMFSLADKDGNGYLSFREFLDILVV   850
 851  FMKGSPEDKSRLMFTMYDLDENGFLSKDEFFTMMRSFIEISNNCLSKAQL   900
 901  AEVVESMFRESGFQDKEELTWEDFHFMLRDHDSELRFTQLCVKGGGGGGN   950
 951  GIRDIFKQNISCRVSFITRTPGERSHPQGLGPPAPEAPELGGPGLKKRFG  1000
1001  KKAAVPTPRLYTEALQEKMQRGFLAQKLQQYKRFVENYRRHIVCVAIFSA  1050
1051  ICVGVFADRAYYYGFASPPSDIAQTTLVGIILSRGTAASVSFMFSYILLT  1100
1101  MCRNLITFLRETFLNRYVPFDAAVDFHRWIAMAAVVLAILHSAGHAVNVY  1150
1151  IFSVSPLSLLACIFPNVFVNDGSKLPQKFYWWFFQTVPGMTGVLLLLVLA  1200
1201  IMYVFASHHFRRRSFRGFWLTHHLYILLYALLIIHGSYALIQLPTFHIYF  1250
1251  LVPAIIYGGDKLVSLSRKKVEISVVKAELLPSGVTYLQFQRPQGFEYKSG  1300
1301  QWVRIACLALGTTEYHPFTLTSAPHEDTLSLHIRAVGPWTTRLREIYSSP  1350
1351  KGNGCAGYPKLYLDGPFGEGHQEWHKFEVSVLVGGGIGVTPFASILKDLV  1400
1401  FKSSLGSQMLCKKIYFIWVTRTQRQFEWLADIIQEVEENDHQDLVSVHIY  1450
1451  VTQLAEKFDLRTTMLYICERHFQKVLNRSLFTGLRSITHFGRPPFEPFFN  1500
1501  SLQEVHPQVRKIGVFSCGPPGMTKNVEKACQLVNRQDRAHFMHHYENF    1548

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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