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

NucPred

Fetching Q09459 from www.uniprot.org...

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

   1  MVSARYPIEKWSRPQLEDHFHNVVEELNKAQKKVKEQEKQITTFNSRFRR    50
  51  SMLERKSQNEKVVERSKYDDVVKENQILDMKLKAAKQQLLIYTAPSARAT   100
 101  TASMMTGRSTFRQPPSTFRQRPPLTAGTTGSIDRPGSAPVARKKSDGGEK   150
 151  LQLATDEKLAIVRLNRTLKNKNDEITELKYTIEKLRQLKSSVNQSSPPTR   200
 201  LSTSSSSKSSSSNNNNDGEGKDSELEEMSEMSDDESGRSTPVIEEKKKPR   250
 251  RKSRKSSHQEPSKNPIPPPRIPDQTEKVLLDKLKVAENDLAMLQEECDLV   300
 301  KKANERLVHQSLSKSTEYGARESIEEKKKIVELEELLKETEKRIKESEHR   350
 351  RREDQKKFEAMRLHYKNKYDAAKKTEKKLSVVAKNSKVEEERIEEEKISH   400
 401  SPPPMTFEPIRKRHSQSEISRMRRADDDLLQKLYKEVADILHSHDVGIAE   450
 451  INTLGASENSLARWQKLYSELYEELEKVRNMLLIQYDINQKQMKEIKLLK   500
 501  DELDRLKTVSAEILSKSREEVEERQKKIFMLEEQIRTIAYSGQQPVKLLA   550
 551  NQINIPTPRVNTDLSVKLINVKPSPSLTSKFFFSLEFFDFQLETTPIMDA   600
 601  KQHNMDFTTVYDVLVSNLLIHYLQTNGIVIEMYRPASDCYKLLAAATISL   650
 651  IPLFEDSVLRKFCSEIMLKSVDTGVEMCTLRYEIEVSQPISDSFKKFKKS   700
 701  EMARNMLPLQLENEDTEDTNFDPLTIMVNRVVGLDTFGKDPSTEFCIVDE   750
 751  FLSFSPYFTDFSTSSEIRSKRDCYIPKIDIARNLFATSSISFFLIENIPR   800
 801  QDGVIATLHLPLHPLCKLGGSIKGTFPMLDTDGRPSSVSLDLCLIWKHEI   850
 851  PSFFLKHEPKEPLKEVKDTPILPQPVRRTSKEFVVTPVKEAELHDAEPTS   900
 901  MPPKAPEPTTAPLRRLSTDSSDTSFSHSSKDLFSPPTNPQTYDYEIPAVT   950
 951  PALVDSDGEEEADRIVFDDDDDEIESVSAVSSQRDPEPLEVPERQVENLP  1000
1001  SPEDTPRPSDPLKPNGTNESKESTPVTQRSVDKTDDVAPVDPELEPESGP  1050
1051  EPEPVVESEPNEVAETEEDRKRELKTEELKSLLGALPPIAKPRNIPVGPI  1100
1101  ALTEQPEATRQQGSTGRILFTDPLHFSVPPSESSSTSSPRRAEKAPVPLP  1150
1151  DYEGHSLIKVRKPLSPTDKDVLEPNMKVSIQLETFELVPGSSLTPLTREE  1200
1201  TTFFVDWVFLDFTNEQSKSTIFDFPRRPQEMVDIRYTKEYTLTRGQLSLL  1250
1251  DQWIRASIKFELTIIKISPGDEEELGFGSLILVPNNTQNKSFVIDVYDRS  1300
1301  GIVQAEMTLTLHFSRALIEQLT                              1322

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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