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

NucPred

Fetching Q02099 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSQHAKRKAGSLDLSPRGLDDRQAFGQLLKEVLALDKEHELGRSNSLPSM    50
  51  TSELVEVLIEVGLLAFKHDDSKSEFISPKMLKEAHLSLQALMLILKRSPT   100
 101  VLREIKSSVTLLDWILPRTISLFADIRFIKLFDSLKEFHKLIYQLISEKS   150
 151  FLWDLYASFMRYWKYYITNVSSIVLQITNATFPYKMPSPNSQPLQSITPN   200
 201  YPTHREDKFDLLIINIEEACTFFFESAHFFAQCSYLKKSNFPSPPLFTAW   250
 251  TWIKPCFFNFVILLKRISIGDSQLFLHLHSRIVQTLCCFSLNFIYHGLPI   300
 301  CEKSKHILMSSINLTLGSLKKTYTVANTAISLFFLSLFVLPKTVAGLFYP   350
 351  FGVSLLSDFKVLEQLEPDSDLKKAIILFKCRYQSSEIDQTTLRAFGEICT   400
 401  GKLENTLFSNSELNLFLLHYLSLDNDLSNILKVDFQNGHNICTFAKWCIN   450
 451  NNLDEPSNLKHFREMLDYYSSHNVTISEDDLKNFSLVLCTHVAKVNEKTN   500
 501  SIFRTYEVHGCEVCNSFCLLFDERSLFKIPYHELFCALLKNPDIISSSVK   550
 551  QSLLLDGFFRWSQHCSNFNKESMLSLREFIMKALASTSRCLRVVAAKVLP   600
 601  IFIKGPNNLDIVEFHKESKALIFNTLKILAVENTAILETVILSWISLSRV   650
 651  VEEEELHFVLLEVISSVINSGIFYQGIGLSALQQIASTRHISVWQLLSPY   700
 701  WPTVSVAIVQGMGKKPNIASLFAQLMNISEGDFLIRTQAYTLPFLVLTKN   750
 751  KALIVRIAELSQSDVATLCLTNMHKILASLLTTDHPNLEESVMLLLSLAT   800
 801  SDFEKVDLTSLLRSDPISITVELLQLYQNDVPHEKIENALRKVAMIVSQV   850
 851  VNDEDLSNKELLYDFFNNHILGILAEFSNILNDLKGKTSINEKIKTIVGI   900
 901  EKMLSLCGGAVKLGLPQILSNLQSAFQNEHLRFYAIKAWFSLILATKEPE   950
 951  YSSIAGLSLVILPPLFPYLEPQEAELVIQIFDFISSDTHKCLQGLKWAIP  1000
1001  TSLDSACFSLKAKEIFCSLQNEDFYSELQSIIKCLTNENEPVCYLGLQKL  1050
1051  ELFFQAKVDELHDTLNLDISNEVLDQLLRCLLDCCVKYASTNMQISYLAA  1100
1101  KNLGELGAIDPSRAKAQHIIKETVVLDNFENGEESLKFILDFMQSQLIPA  1150
1151  FLVTTDTKAQGFLAYALQEFLKLGGFKSAVINKKKGLTVVTEHWMSLPDL  1200
1201  SKRVLIPFLTSKYHLTPIPKIDIRYPIYKENVTIHTWMQLFSLKLMEYAH  1250
1251  SQNAEKIFGICSKVVKDQEVNIPCFLLPFLVLNVILTESELEVNKVIEEF  1300
1301  QLVINQPGPDGLNSVGQQRYTSFVDVFFKIVDYLNKWLRMRKKRNWDRRS  1350
1351  AIARKENRYMSVEDATSRESSISKVESFLSRFPSKTLGIVSLNCGFHARA  1400
1401  LFYWEQHIRNATAPYAALESDYRVLQEIYAGIDDPDEIEAVSLNFHDYSF  1450
1451  DQQLLLHENSGTWDSALSCYEIIIQKDPENKKAKIGLLNSMLQSGHYESL  1500
1501  VLSLDSFIINDNHEYSKMLNLGIEASWRSLSIDSLKKCLSKSNLESFEAK  1550
1551  LGSIFYQYLRKDSFAELTERLQPLYVDAATAIANTGAHSAYDCYDILSKL  1600
1601  HAINDFSRIAETDGIVSDNLDIVLRRRLSQVAPYGKFKHQILSTHLVGYE  1650
1651  KFENTKKTAEIYLEIARISRKNGQFQRAFNAILKAMDLDKPLATIEHAQW  1700
1701  WWHQGQHRKAISELNFSLNNNMFDLVDEHEERPKNRKETLGNPLKGKVFL  1750
1751  KLTKWLGKAGQLGLKDLETYYHKAVEIYSECENTHYYLGHHRVLMYEEEQ  1800
1801  KLPVNEQSERFLSGELVTRIINEFGRSLYYGTNHIYESMPKLLTLWLDFG  1850
1851  AEELRLSKDDGEKYFREHIISSRKKSLELMNSNVCRLSMKIPQYFFLVAL  1900
1901  SQMISRVCHPNNKVYKILEHIIANVVASYPGETLWQLMATIKSTSQKRSL  1950
1951  RGKSILNVLHSRKLSMSSKVDIKALSQSAILITEKLINLCNTRINSKSVK  2000
2001  MSLKDHFRLSFDDPVDLVIPAKSFLDITLPAKDANRASHYPFPKTQPTLL  2050
2051  KFEDEVDIMNSLQKPRKVYVRGTDGNLYPFLCKPKDDLRKDARLMEFNNL  2100
2101  ICKILRKDQEANRRNLCIRTYVVIPLNEECGFIEWVNHTRPFREILLKSY  2150
2151  RQKNIPISYQEIKVDLDFALRSPNPGDIFEKKILPKFPPVFYEWFVESFP  2200
2201  EPNNWVTSRQNYCRTLAVMSIVGYVLGLGDRHGENILFDEFTGEAIHVDF  2250
2251  NCLFDKGLTFEKPEKVPFRLTHNMVDAMGPTGYEGGFRKASEITMRLLRS  2300
2301  NQDTLMSVLESFLHDPLVEWNRKKSSSKYPNNEANEVLDIIRKKFQGFMP  2350
2351  GETIPLSIEGQIQELIKSAVNPKNLVEMYIGWAAYF                2386

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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