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

NucPred

Fetching O19906 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MISISKRTSIARINLSEFHTISKIDRYPWLNKEKDACGVGFIAHLDNKFG    50
  51  HKLMMNALEALATMEHRGACSADEESGDGAGILFSIPWKFFVEWSLRYKQ   100
 101  FKINISQAAVAMLFLPCLSSDIQVSKNIVEEIFQDEDFIVIGWREVPYVK   150
 151  EVLGPLALRNMPQIYQIVVQSKRYQGRSLDFHLYRVRRKIEKEITVRAYS   200
 201  WAKDFYFCSCSNHTIVYKGMVKSTSLGQFYQDLYNPDFEISFAVFHRRFS   250
 251  TNTMPRWPLAQPMRILGHNGEINTLLGNLKWMEARESSLNHPTLNEVASI   300
 301  GPVVNVSNSDSANLDSVVELFLHVGHSCPEALMFLIPEAYENNPKLKYHQ   350
 351  NLISFYEYCAGFQEAWDGPALIVFSDGHTVGASLDRNGLRPARYCVTEDN   400
 401  VLILASEGGVLNLDPSLIRLKGRLGPGEMIVLDLQEKLLMSNLEIKNKIA   450
 451  SLRPYSDWIKQNRQVLIPTSFLTSTTLPLQEVFKRQTCFGYTSEDIELVI   500
 501  ENMAIQGKEPTFCMGDDTPLAVLSGKSHVLYDYFKQRFAQVTNPPIDSLR   550
 551  ESLVMSISSYLGSKTNSFEESSEKILKIKTPILSENDLVLIKNSELLTET   600
 601  LVTTFEAHFDSPQANGQSLFSTINQLCKQAKNLIQAGTKIIILSDKVCFE   650
 651  SRTESYIPPLLVVGSLHQYLIKQGVRQKVSLIVETGQCWSTHHFACLLGY   700
 701  GASAVCPYLALETVRHWWMSERTQNLMSKGKMPNLTLIEVQNNYCKSVER   750
 751  GLLKILSKMGISLLTSYIGAQIFEILGLGKEVVDLAFEGTVSRIGGLSFA   800
 801  DLAMETIDLCSAGFSKLNKKKLDNHGFVQYRPGGEYHLNNPEMSKALHKA   850
 851  VRENNYTLYEAYKQLLANRPPTNIRDLLEFNFRSCSVPLEKVENIFEITK   900
 901  RFCTGGMSLGALSREAHETLSIAMNRIGGKSNSGEGGEDSLRFTVLTDVD   950
 951  ETGNSPSFPHLKGLKNGDSLSSAIKQIASGRFGVTPEYLVNAKQLEIKIS  1000
1001  QGAKPGEGGQLPGKKVSPYIATLRACKPGVTLISPPPHHDIYSIEDLAQL  1050
1051  IFDLHQVNPECKVSVKLVSEIGVGTIAVGVAKAGAEIIQISGHDGGTGAS  1100
1101  PLSSIKHAGVPWELGLHEVHCLLVENNLREKVILRVDGGLRTGQDVVMAA  1150
1151  LLGADEYGFGTIAMIAGGCIMARVCHTNSCPVGVATQKEELRMRYPGVPE  1200
1201  NVVNYFIFLAEEIRVILSKLGFETLSQIIGRKDLINHNFDKKLCKTHCID  1250
1251  TSIFFNIKTNEYNFLEIPGGHSKKLKTSLLDYELLNSSDILYAIDNHKTL  1300
1301  EKHIKISNSDRSVGAKLAGRLAKQYKNEGFRGSLILNFYGTAGQSFGSFN  1350
1351  IKGVTLRLIGEANDYVGKSMSGGEIVIVPPSEVAFDASEQVILGNTCLYG  1400
1401  ATGGFLFAYGAAGERFAVRNSNAFSVLEGVGDHACEYMTGGRVVVLGKAG  1450
1451  RNIAAGMTGGIAYFLDEYSNLPEKVNLDIVRIQRVVTNEARKQLIQLIEK  1500
1501  HVLKTGSKKAVLILQQWEIFIHYFWQIVPPSESETSETNYFVENKVLAN   1549

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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