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

NucPred

Fetching O94421 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MFAVQGNQKFPKGLTKDNIQSLYQQWQVMRNQGATEENNPEFAQISSILR    50
  51  MVQRAHYARMQQMRNQSSEFPDAENTNLRKQQDTLPTTGFNNLPEGKAGM   100
 101  QTLPGRPASNGPTPPNPGNGNVGLNNPSYMNSQASPNIMNAPLQRDTSVP   150
 151  PAPSMVHPHTNTNANSNNLKVYANQLSQQNTSNPTYHNAYDMASMMKNGS   200
 201  RMNNSFPPTTPYPPANDTTVNSSLPHSFASPSSTFEQPHTVQSRAPSVDT   250
 251  TSSSHSFSARNIPANVSMQQQMGRRGSIPVNPSTFSASSPPSGSMLASPY   300
 301  NGYQNDAASFAHSKLPSSANPNTPFNSTATVDVGAAGSHFPYPQPSNLDA   350
 351  INAKTYFQSSSNSPAPYVYRNNLPPSATSFQPSSSRSPSVDPNTVKSAQH   400
 401  IPRMSPSPSASALKTQSHVPSAKVPPTSKLNHAQLAMLKSQIVAYNCLNS   450
 451  PNGQVPPAVQQAIFGRVYGASNEVSPSMPFQQNVPQMSSVKKDTPTRDAN   500
 501  MRTSKAPYIQNIPNQFQRRAYSATIPVKNESLAKPSVSPMPLQQSTGKTE   550
 551  VAKRAQFPTNVNYSSCVDPRTYVKTPIPFSKFSSSENLSLIPSLLPPSIS   600
 601  WDDVFLSSEIAIACSIANRIDFLEKENRPKSVNKKILQQDKSKSMIELRC   650
 651  LRLLEKQRSLRETINSVIPHSDSLAAGNLRLMFRNVKRQTMQEANLVLAL   700
 701  AEKQKTEHAMRQKEKLLTHLRSIMLHRKSIVTKVDKQNKAKTQRCKDIIN   750
 751  FHAHLEKEEKKRIERSARQRLQALRADDEAAYLQLLDKAKDTRITHLLKQ   800
 801  TDQYLENLTRAVRIQQSNIHSGNTSGKGSNSAELEAPISEEDKNLDYFKV   850
 851  AHRIHEEVEQPKIFVGGTLKDYQLKGLEWMLSLYNNNLNGILADEMGLGK   900
 901  TIQTIAFITYLIEKKNQQGPFLIIVPLSTLTNWIMEFEKWAPSVKKIAYK   950
 951  GPPQLRKTLQSQIRSSNFNVLLTTFEYIIKDRPLLSRIKWVHMIIDEGHR  1000
1001  IKNTQSKLTSTLSTYYHSQYRLILTGTPLQNNLPELWALLNFVLPKIFNS  1050
1051  IKSFDEWFNTPFANTGGQDKIGLNEEEALLIIKRLHKVLRPFLFRRLKKD  1100
1101  VEKELPDKVEKVIKCPLSGLQLKLYQQMKKHGMLFVDGEKGKTGIKGLQN  1150
1151  TVMQLKKICNHPFIFEDVERAIDPSGTNVDLLWRAAGKFELLDRILPKLF  1200
1201  LTGHKTLMFFQMTQIMTIMEDYLRSKNWKYLRLDGSTKSDDRCSLLAQFN  1250
1251  DPKSDVYIFMLSTRAGGLGLNLQTADTVIIFDTDWNPHQDLQAQDRAHRI  1300
1301  GQTKEVRILRLITEKSIEENILSRAQYKLDLDGKVIQAGKFDNKSTPEER  1350
1351  EAFLRSLLEHDGDDDHDLTYGELQDDELNELISRTDEELVLFKKLDKERA  1400
1401  ATDIYGKGKPLERLLTVNELPDFYKVEVDSFAVQSSSELEDQYLERKRRR  1450
1451  RNSISYTELTLDELNTVDDPSSTLMPRKRGRPRKKTNSGSSLSTPLSQES  1500
1501  SLARSGRKNTPSYKQKALRRYCMEIFERLYNLQSEDGRFVNGLFLYPPNR  1550
1551  KLYPDYYIIIKRPIALGKIKRNIKNDRYGDVGELIADFMLMFNNAYTYNE  1600
1601  EHSIVYEDAKLMEKTLKEVIEDLEKNNSLHAYEEEALNEEQASLVFLENS  1650
1651  EAELPLDSGIVSAEDDKVITYEDSSSSYSE                      1680

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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