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

NucPred

Fetching Q5SXM2 from www.uniprot.org...

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

   1  MDVDAEREKITQEIKELERILDPGSSGSHVEISESSLESDSEADSLPSED    50
  51  LDPADPPISEEERWGEASNDEDDPKDKTLPEDPETCLQLNMVYQEVIQEK   100
 101  LAEANLLLAQNREQQEELMRDLAGSKGTKVKDGKSLPPSTYMGHFMKPYF   150
 151  KDKVTGVGPPANEDTREKAAQGIKAFEELLVTKWKNWEKALLRKSVVSDR   200
 201  LQRLLQPKLLKLEYLHQKQSKVSSELERQALEKQGREAEKEIQDINQLPE   250
 251  EALLGNRLDSHDWEKISNINFEGSRSAEEIRKFWQNSEHPSINKQEWSRE   300
 301  EEERLQAIAAAHGHLEWQKIAEELGTSRSAFQCLQKFQQHNKALKRKEWT   350
 351  EEEDRMLTQLVQEMRVGSHIPYRRIVYYMEGRDSMQLIYRWTKSLDPGLK   400
 401  KGYWAPEEDAKLLQAVAKYGEQDWFKIREEVPGRSDAQCRDRYLRRLHFS   450
 451  LKKGRWNLKEEEQLIELIEKYGVGHWAKIASELPHRSGSQCLSKWKIMMG   500
 501  KKQGLRRRRRRARHSVRWSSTSSSGSSSGSSGGSSSSSSSSSEEDEPEQA   550
 551  QAGEGDRALLSPQYMVPDMDLWVPARQSTSQPWRGGAGAWLGGPAASLSP   600
 601  PKGSSASQGGSKEASTTAAAPGEETSPVQVPARAHGPVPRSAQASHSADT   650
 651  RPAGAEKQALEGGRRLLTVPVETVLRVLRANTAARSCTQKEQLRQPPLPT   700
 701  SSPGVSSGDSVARSHVQWLRHRATQSGQRRWRHALHRRLLNRRLLLAVTP   750
 751  WVGDVVVPCTQASQRPAVVQTQADGLREQLQQARLASTPVFTLFTQLFHI   800
 801  DTAGCLEVVRERKALPPRLPQAGARDPPVHLLQASSSAQSTPGHLFPNVP   850
 851  AQEASKSASHKGSRRLASSRVERTLPQASLLASTGPRPKPKTVSELLQEK   900
 901  RLQEARAREATRGPVVLPSQLLVSSSVILQPPLPHTPHGRPAPGPTVLNV   950
 951  PLSGPGAPAAAKPGTSGSWQEAGTSAKDKRLSTMQALPLAPVFSEAEGTA  1000
1001  PAASQAPALGPGQISVSCPESGLGQSQAPAASRKQGLPEAPPFLPAAPSP  1050
1051  TPLPVQPLSLTHIGGPHVATSVPLPVTWVLTAQGLLPVPVPAVVSLPRPA  1100
1101  GTPGPAGLLATLLPPLTETRAAQGPRAPALSSSWQPPANMNREPEPSCRT  1150
1151  DTPAPPTHALSQSPAEADGSVAFVPGEAQVAREIPEPRTSSHADPPEAEP  1200
1201  PWSGRLPAFGGVIPATEPRGTPGSPSGTQEPRGPLGLEKLPLRQPGPEKG  1250
1251  ALDLEKPPLPQPGPEKGALDLGLLSQEGEAATQQWLGGQRGVRVPLLGSR  1300
1301  LPYQPPALCSLRALSGLLLHKKALEHKATSLVVGGEAERPAGALQASLGL  1350
1351  VRGQLQDNPAYLLLRARFLAAFTLPALLATLAPQGVRTTLSVPSRVGSES  1400
1401  EDEDLLSELELADRDGQPGCTTATCPIQGAPDSGKCSASSCLDTSNDPDD  1450
1451  LDVLRTRHARHTRKRRRLV                                 1469

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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