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

NucPred

Fetching Q6R2W3 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MEAVSRVFPALAGQAPEEQGEIIKVKVKEEDHTWDQESALRRNLSYTREL    50
  51  SRQRFRQFCYQETPGPREALSQLRELCRQWLNPEIHTKEQILELLVLEQF   100
 101  LTILPEELQSWVREHNPESGEEVVTLLEDLERELDEPRQQVSQGTYGQEV   150
 151  SMEEMIPLDSAKESLGTQLQSMEDRMECESPEPHPLQDNGSFLWFSMMSQ   200
 201  SMGGDNLSSLDTNEAEIEPENMREKFFRSLARLLENKSNNTKIFSKAKYC   250
 251  QLIKEVKEAKAKAKKESVDYRRLARFDVILVQGNEKLIEAVNGETDKIRY   300
 301  YLHSEDLFDILHNTHLSIGHGGRTRMEKELQAKYKNITKEVIMLYLTLCK   350
 351  PCQQKNSKLKKVLTSKSIKEVSSRCQVDLIDMQLNPDGEYRFILHYQDLC   400
 401  TKLTFLRSLKSKRPTEVAHALLDIFTIIGAPSVLQSDNGREFSSQVVSEL   450
 451  SNIWPELKIVHGKSQTCQSQSSAEQTEDIRKRIFSWMQTNNSSHWTEFLW   500
 501  FIQMSQNQPYHRSMQQTPCESAFSSEAKLGLSHSQLTEELVASLHTENEL   550
 551  DQADKELENTLRAQYEENIETGTDSSDIEENLSVTPKVAEKSPPESRLRF   600
 601  LSCVVCEKECTGVNSCISCDGNIHAICGVPSQHGTEGCGRQITCSLCYET   650
 651  STMKRKHDEIQRSLPVKPSKMLKPSGTPFSPDKVGDWMAKQASLDFFVKK   700
 701  RHAFSEHSSSNKRNVNNRSYPEEGKTKRVHASFTRKYDPSYIEFGFVAVI   750
 751  DGEVLKPQCIICGDVLANEAMKPSKLKRHLYSKHKEISSQPKEFFERKSS   800
 801  ELKSQPKQVFNVSHINISALRASYKVALPVAKSKTPYTIAETLVKDCIKE   850
 851  VCLEMLGESAAKKVAQVPLSNDTIARRIQELANDMEDQLIEQIKLAKYFS   900
 901  LQLDECRDIANMIILLVYVRFEHDDDIKEEFFFSASLPTNTTSSELYEAV   950
 951  KNYIVNKCGLEFKFCVGVCSDGAASMTGKHSEVVTQIKELAPECKTTHCF  1000
1001  IHRESLAMKKISAELNSVLNDIVKIVNYIKSNSLNSRLFSLLCDNMEADH  1050
1051  KQLLLHAEIRWLSRGKVLSRMFEIRNELLVFLQGKKPMWSQLFKDVNWTA  1100
1101  RLAYLSDIFSIFNDLNASMQGKNATYFSMADKVEGQKQKLEAWKNRISTD  1150
1151  CYDMFHNLTTIINEVGNDLDIAHLRKVISEHLTNLLECFEFYFPSKEDPR  1200
1201  IGNLWIQNPFLSSKDNLNLTVTLQDKLLKLATDEGLKISFENTASLPSFW  1250
1251  IKAKNDYPELAEIALKLLLLFPSTYLCETGFSTLSVIKTKHRNSLNIHYP  1300
1301  LRVALSSIQPRLDKLTSKKQAHLSH                           1325

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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