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

NucPred

Fetching P20740 from www.uniprot.org...

The NucPred score for your sequence is 0.46 (see score help below)

   1  MHCFLGREILSFFCLTVRKMWLKFILAILLLHAAAGKEPEPQYVLMVPAV    50
  51  LQSDSPSQVCLQFFNLNQTISVRVVLEYDTINTTIFEKNTTTSNGLQCLN   100
 101  FMIPPVTSVSLAFISFTAKGTTFDLKERRSVMIWNMESFVFVQTDKPIYK   150
 151  PGQSVMFRVVALDFNFKPVQEMYPLIAVQDPQNNRIFQWQNVTSEINIVQ   200
 201  IEFPLTEEPILGNYKIIVTKKSGERTSHSFLVEEYVLPKFDVTVTAPGSL   250
 251  TVMDSELTVKICAVYTYGQPVEGKVQLSVCRDFDSYGRCKKSPVCQSFTK   300
 301  DLDTDGCLSHILSSKVFELNRIGYKRNLDVKAIVTEKEQVCNLTATQSIS   350
 351  ITQVMSSLQFENVDHHYRRGIPYFGQIKLVDKDNSPISNKVIQLFVNNKN   400
 401  THNFTTDINGIAPFSIDTSKIFDPELSLKALYKTSDQCHSEGWIEPSYPD   450
 451  ASLSVQRLYSWTSSFVRIEPLWKDMSCGQKRMITVYYILNTEGYEHINIV   500
 501  NFYYVGMAKGKIVLTGEIKVNIQADQNGTFMIPLVVNEKMAPALRLLVYM   550
 551  LHPAKELVADSVRFSIEKCFKNKVQLQFSEKQMLTTSNVSLVIEAAANSF   600
 601  CAVRAVDKSMLLLKSETELSAETIYNLHPIQDLQGYIFNGLNLEDDPQDP   650
 651  CVSSDDIFHKGLYYRPLTSGLGPDVYQFLRDMGMKFFTNSKIRQPTVCTR   700
 701  ETVRPPSYFLNAGFTASTHHVKLSAEVAREERGKRHILETIREFFPETWI   750
 751  WDIILINSTGKASVSYTIPDTITEWKASAFCVEELAGFGMSVPATLTAFQ   800
 801  PFFVDLTLPYSIIHGEDFLVRANVFNYLNHCIKINVLLLESLDYQAKLIS   850
 851  PEDDGCVCAKIRKSYVWNIFPKGTGDVLFSITAETNDDEACEEEALRNIR   900
 901  IDYRDTQIRALLVEPEGIRREETQNFLICMKDDVISQDVAIDLPTNVVEG   950
 951  SPRPSFSVVGDIMGTAIQNVHQLLQMPFGNGEQNMVLFAPNIYVLDYLDK  1000
1001  TRQLSEDVKSKTIGYLVSGYQKQLSYKHPDGSYSTFGIRDKEGNTWLTAF  1050
1051  VYKSFAEASRFIYIDDNVQAQTLIWLATKQKTDGCFQSTGILVNNAMKGG  1100
1101  VENELSLSAYITIALLEAGHSMSHTVIRNAFYCLETASEKNITDIYTQAL  1150
1151  VAYAFCLAGKAEICESFLRELQKSAKEVDGSKYWEQNQRSAPEKSHLLDH  1200
1201  VQSTDVEITSYVLLALLYKPNRSQEDLTKASAIVQWIIRQQNSYGGFASM  1250
1251  QDTVVALQALAAYGAATYNSVTQNVIKINSKNTFEKVFTVNNENRLLLQQ  1300
1301  TPLPQVPGKYSLTVNGTGCVLIQTALRYNIHLPEGAFGFSLSVQTSNASC  1350
1351  PRDQPGKFDIVLISSYTGKRSSSNMVIIDVKMLSGFVPVKSSLDQLIDDH  1400
1401  TVMQVEYKKNHVLLYLGNILQKRRKEVTFSVEQDFVVTHPKPAPVQIYDY  1450
1451  YETEEYAVAEYMSLCRGVVEEMG                             1473

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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