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

NucPred

Fetching Q9BX26 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MPIRPDLQQLEKCIDDALRKNDFKPLKTLLQIDICEDVKIKCSKQFFHKV    50
  51  DNLICRELNKEDIHNVSAILVSVGRCGKNISVLGQAGLLTMIKQGLIQKM   100
 101  VAWFEKSKDIIQSQGNSKDEAVLNMIEDLVDLLLVIHDVSDEGKKQVVES   150
 151  FVPRICSLVIDSRVNICIQQEIIKKMNAMLDKMPQDARKILSNQEMLILM   200
 201  SSMGERILDAGDYDLQVGIVEALCRMTTEKQRQELAHQWFSMDFIAKAFK   250
 251  RIKDSEFETDCRIFLNLVNGMLGDKRRVFTFPCLSAFLDKYELQIPSDEK   300
 301  LEEFWIDFNLGSQTLSFYIAGDNDDHQWEAVTVPEEKVQIYSIEVRESKK   350
 351  LLTIILKNTVKISKREGKELLLYFDASLEITNVTQKIFGATKHRESIRKQ   400
 401  GISVAKTSLHILFDASGSQILVPESQISPVGEELVSLKEKSKSPKEFAKP   450
 451  SKYIKNSDKGNRNNSQLEKTTPSKRKMSEASMIVSGADRYTMRSPVLFSN   500
 501  TSIPPRRRRIKPPLQMTSSAEKPSVSQTSENRVDNAASLKSRSSEGRHRR   550
 551  DNIDKHIKTAKCVENTENKNVEFPNQNFSELQDVIPDSQAAEKRDHTILP   600
 601  GVLDNICGNKIHSKWACWTPVTNIELCNNQRASTSSGDTLNQDIVINKKL   650
 651  TKQKSSSSISDHNSEGTGKVKYKKEQTDHIKIDKAEVEVCKKHNQQQNHP   700
 701  KYSGQKNTENAKQSDWPVESETTFKSVLLNKTIEESLIYRKKYILSKDVN   750
 751  TATCDKNPSASKNVQSHRKAEKELTSELNSWDSKQKKMREKSKGKEFTNV   800
 801  AESLISQINKRYKTKDDIKSTRKLKESLINSGFSNKPVVQLSKEKVQKKS   850
 851  YRKLKTTFVNVTSECPVNDVYNFNLNGADDPIIKLGIQEFQATAKEACAD   900
 901  RSIRLVGPRNHDELKSSVKTKDKKIITNHQKKNLFSDTETEYRCDDSKTD   950
 951  ISWLREPKSKPQLIDYSRNKNVKNHKSGKSRSSLEKGQPSSKMTPSKNIT  1000
1001  KKMDKTIPEGRIRLPRKATKTKKNYKDLSNSESECEQEFSHSFKENIPVK  1050
1051  EENIHSRMKTVKLPKKQQKVFCAETEKELSKQWKNSSLLKDAIRDNCLDL  1100
1101  SPRSLSGSPSSIEVTRCIEKITEKDFTQDYDCITKSISPYPKTSSLESLN  1150
1151  SNSGVGGTIKSPKNNEKNFLCASESCSPIPRPLFLPRHTPTKSNTIVNRK  1200
1201  KISSLVLTQETQNSNSYSDVSSYSSEERFMEIESPHINENYIQSKREESH  1250
1251  LASSLSKSSEGREKTWFDMPCDATHVSGPTQHLSRKRIYIEDNLSNSNEV  1300
1301  EMEEKGERRANLLPKKLCKIEDADHHIHKMSESVSSLSTNDFSIPWETWQ  1350
1351  NEFAGIEMTYETYERLNSEFKRRNNIRHKMLSYFTTQSWKTAQQHLRTMN  1400
1401  HQSQDSRIKKLDKFQFIIIEELENFEKDSQSLKDLEKEFVDFWEKIFQKF  1450
1451  SAYQKSEQQRLHLLKTSLAKSVFCNTDSEETVFTSEMCLMKEDMKVLQDR  1500
1501  LLKDMLEEELLNVRRELMSVFMSHERNANV                      1530

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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