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

NucPred

Fetching Q9ES45 from www.uniprot.org...

The NucPred score for your sequence is 0.53 (see score help below)

   1  MLPTSLKTLVLLGALLTGPLGPAGGQDAPSLPREVQRYDGWFNNLKYHQR    50
  51  GAAGSQLRRLVPANYADGVYQALQEPLLPNARLLSDAVSKGKAGLPSAHN   100
 101  RTVLGLFFGYHVLSDLVSVETPGCPAEFLNIYIPRGDPVFDPDKRGNVVL   150
 151  PFQRSRWDRSTGQSPSNPRDLTNQVTGWLDGSAIYGSSHSWSDTLRSFSG   200
 201  GQLASGPDPAFPRNSQNSLLMWMAPDPATGQGGPQGLYAFGAQRGNREPF   250
 251  LQALGLLWFRYHNLCAKRLAQEHPHWGDEELFQHARKRVIATYQNIALYQ   300
 301  WLPSFLQKTPPEYSGYRPFMDPSISPEFVAASEQFLSTMVPPGVYMRNSS   350
 351  CHFREFPKEGSSSSPALRVCNNYWIRENPSLKTAQDVDQLLLGMASQISE   400
 401  LEDRIVIEDLRDYWPGPDRYSRTDYVASSIQSGRDMGLPSYSQALQALGL   450
 451  EPPKNWSALNPKVDPQVLEATAALYNQDLSRLELFLGGLLESHGDPGPLF   500
 501  SNIILDQFVRLRDGDRYWFENTRNGLFSKEEIAEIRNTTLRDVLVAVSNV   550
 551  DPSALQPNVFFWQEGAPCPQPQQLTTEGLPQCVPVTVIDYFEGSGAGYGV   600
 601  TLLAVCCFPVVSLIIAWVVARFRNRERKMLLKKGKESLKKQTASDGVPAM   650
 651  EWPGPKESSYPVTVQLLPDRSLKVLDKRLTVLRTIQLQPTQQVNLILSSS   700
 701  HGRRTLLLKIPKEYDLVLMFNSEEDRDAFVQLLQDLCVCSTPGLRIAEMD   750
 751  EKELLRKAVTKQQRAGILEIFFRQLFAQVLDINQADAGTLPLDSSQQVRE   800
 801  ALTCELSRAEFADSLGLKPQDMFVESMFSLADKDGNGYISFREFLDILVV   850
 851  FMKGSPQDKSRLMFTMYDLDGNGFLSKEEFFTMMRSFIEISNNCLSKDQL   900
 901  AEVVESMFRESGFQDKEELTWEDFHFMLRDHDSDLRFTQLCVKGGAGGTG   950
 951  DIFKQSNACRVSFLTRTPGNRVMAPSPRLYTEALQEKMQRGFLAQKLKQF  1000
1001  KRFVENYRRHIVCVTIFSAICAGLFADRAYYYGFASPPTDIEETTYVGII  1050
1051  LSRGTAASISFMFSYILLTMCRNLITFLRETFLNRYIPFDAAVDFHRWIA  1100
1101  MAAVVLAVVHSLGHAVNVYIFSVSPLSLMTCVFPSVFVNDGSKLPPKYYW  1150
1151  WFFETVPGMTGVLLLLVLAIMYVFASHHFRRHSFRGFWLTHHLYVVLYAL  1200
1201  IIIHGSYALIQLPSFHIYFLVPAIIYVGDKLVSLSRKKVEISVVKVELLP  1250
1251  SGVTYLQFQRPKTFEYKSGQWVRIACLSLGTNEYHPFTLTSAPHEDTLSL  1300
1301  HIRAVGPWTTRLREIYSPPVGGTSARYPKLYLDGPFGEGHQEWHKFEVSV  1350
1351  LVGGGIGVTPFASILKDLVFKSSMGTQMLCKKIYFIWVTRTQRQFEWLAD  1400
1401  IIREVEENGSRDLVSVHIYITQLAEKFDLRTTMLYICERHFQKVLNRSLF  1450
1451  TGLRSVTHFGRPPFELFLDSLQEVHPQVHKIGVFSCGPPGMTKNVEKACQ  1500
1501  LINRQDRAHFVHHYENF                                   1517

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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