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

NucPred

Fetching Q9BQS8 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MASTNAESQLQRIIRDLQDAVTELSKEFQEAGEPITDDSTSLHKFSYKLE    50
  51  YLLQFDQKEKATLLGNKKDYWDYFCACLAKVKGANDGIRFVKSISELRTS   100
 101  LGKGRAFIRYSLVHQRLADTLQQCFMNTKVTSDWYYARSPFLQPKLSSDI   150
 151  VGQLYELTEVQFDLASRGFDLDAAWPTFARRTLTTGSSAYLWKPPSRSSS   200
 201  MSSLVSSYLQTQEMVSNFDLNSPLNNEALEGFDEMRLELDQLEVREKQLR   250
 251  ERMQQLDRENQELRAAVSQQGEQLQTERERGRTAAEDNVRLTCLVAELQK   300
 301  QWEVTQATQNTVKELQTCLQGLELGAAEKEEDYHTALRRLESMLQPLAQE   350
 351  LEATRDSLDKKNQHLASFPGWLAMAQQKADTASDTKGRQEPIPSDAAQEM   400
 401  QELGEKLQALERERTKVEEVNRQQSAQLEQLVKELQLKEDARASLERLVK   450
 451  EMAPLQEELSGKGQEADQLWRRLQELLAHTSSWEEELAELRREKKQQQEE   500
 501  KELLEQEVRSLTRQLQFLETQLAQVSQHVSDLEEQKKQLIQDKDHLSQQV   550
 551  GMLERLAGPPGPELPVAGEKNEALVPVNSSLQEAWGKPEEEQRGLQEAQL   600
 601  DDTKVQEGSQEEELRQANRELEKELQNVVGRNQLLEGKLQALQADYQALQ   650
 651  QRESAIQGSLASLEAEQASIRHLGDQMEASLLAVRKAKEAMKAQMAEKEA   700
 701  ILQSKEGECQQLREEVEQCQQLAEARHRELRALESQCQQQTQLIEVLTAE   750
 751  KGQQGVGPPTDNEARELAAQLALSQAQLEVHQGEVQRLQAQVVDLQAKMR   800
 801  AALDDQDKVQSQLSMAEAVLREHKTLVQQLKEQNEALNRAHVQELLQCSE   850
 851  REGALQEERADEAQQREEELRALQEELSQAKCSSEEAQLEHAELQEQLHR   900
 901  ANTDTAELGIQVCALTVEKERVEEALACAVQELQDAKEAASREREGLERQ   950
 951  VAGLQQEKESLQEKLKAAKAAAGSLPGLQAQLAQAEQRAQSLQEAAHQEL  1000
1001  NTLKFQLSAEIMDYQSRLKNAGEECKSLRGQLEEQGRQLQAAEEAVEKLK  1050
1051  ATQADMGEKLSCTSNHLAECQAAMLRKDKEGAALREDLERTQKELEKATT  1100
1101  KIQEYYNKLCQEVTNRERNDQKMLADLDDLNRTKKYLEERLIELLRDKDA  1150
1151  LWQKSDALEFQQKLSAEERWLGDTEANHCLDCKREFSWMVRRHHCRICGR  1200
1201  IFCYYCCNNYVLSKHGGKKERCCRACFQKLSEGPGSPDSSGSGTSQGEPS  1250
1251  PALSPASPGPQATGGQGANTDYRPPDDAVFDIITDEELCQIQESGSSLPE  1300
1301  TPTETDSLDPNAAEQDTTSTSLTPEDTEDMPVGQDSEICLLKSGELMIKV  1350
1351  PLTVDEIASFGEGSRELFVRSSTYSLIPITVAEAGLTISWVFSSDPKSIS  1400
1401  FSVVFQEAEDTPLDQCKVLIPTTRCNSHKENIQGQLKVRTPGIYMLIFDN  1450
1451  TFSRFVSKKVFYHLTVDRPVIYDGSDFL                        1478

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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