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

NucPred

Fetching Q8TDI0 from www.uniprot.org...

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

   1  MRGPVGTEEELPRLFAEEMENEDEMSEEEDGGLEAFDDFFPVEPVSLPKK    50
  51  KKPKKLKENKCKGKRKKKEGSNDELSENEEDLEEKSESEGSDYSPNKKKK   100
 101  KKLKDKKEKKAKRKKKDEDEDDNDDGCLKEPKSSGQLMAEWGLDDVDYLF   150
 151  SEEDYHTLTNYKAFSQFLRPLIAKKNPKIPMSKMMTVLGAKWREFSANNP   200
 201  FKGSSAAAAAAAVAAAVETVTISPPLAVSPPQVPQPVPIRKAKTKEGKGP   250
 251  GVRKKIKGSKDGKKKGKGKKTAGLKFRFGGISNKRKKGSSSEEDEREESD   300
 301  FDSASIHSASVRSECSAALGKKSKRRRKKKRIDDGDGYETDHQDYCEVCQ   350
 351  QGGEIILCDTCPRAYHLVCLDPELEKAPEGKWSCPHCEKEGIQWEPKDDD   400
 401  DEEEEGGCEEEEDDHMEFCRVCKDGGELLCCDACPSSYHLHCLNPPLPEI   450
 451  PNGEWLCPRCTCPPLKGKVQRILHWRWTEPPAPFMVGLPGPDVEPSLPPP   500
 501  KPLEGIPEREFFVKWAGLSYWHCSWVKELQLELYHTVMYRNYQRKNDMDE   550
 551  PPPFDYGSGDEDGKSEKRKNKDPLYAKMEERFYRYGIKPEWMMIHRILNH   600
 601  SFDKKGDVHYLIKWKDLPYDQCTWEIDDIDIPYYDNLKQAYWGHRELMLG   650
 651  EDTRLPKRLLKKGKKLRDDKQEKPPDTPIVDPTVKFDKQPWYIDSTGGTL   700
 701  HPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKEGHSKG   750
 751  PYLVSAPLSTIINWEREFEMWAPDFYVVTYTGDKESRSVIRENEFSFEDN   800
 801  AIRSGKKVFRMKKEVQIKFHVLLTSYELITIDQAILGSIEWACLVVDEAH   850
 851  RLKNNQSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNN   900
 901  LEGFLEEFADISKEDQIKKLHDLLGPHMLRRLKADVFKNMPAKTELIVRV   950
 951  ELSQMQKKYYKFILTRNFEALNSKGGGNQVSLLNIMMDLKKCCNHPYLFP  1000
1001  VAAVEAPVLPNGSYDGSSLVKSSGKLMLLQKMLKKLRDEGHRVLIFSQMT  1050
1051  KMLDLLEDFLEYEGYKYERIDGGITGGLRQEAIDRFNAPGAQQFCFLLST  1100
1101  RAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRIGQNKKVMIYRFVT  1150
1151  RASVEERITQVAKRKMMLTHLVVRPGLGSKSGSMTKQELDDILKFGTEEL  1200
1201  FKDDVEGMMSQGQRPVTPIPDVQSSKGGNLAASAKKKHGSTPPGDNKDVE  1250
1251  DSSVIHYDDAAISKLLDRNQDATDDTELQNMNEYLSSFKVAQYVVREEDG  1300
1301  VEEVEREIIKQEENVDPDYWEKLLRHHYEQQQEDLARNLGKGKRIRKQVN  1350
1351  YNDASQEDQEWQDELSDNQSEYSIGSEDEDEDFEERPEGQSGRRQSRRQL  1400
1401  KSDRDKPLPPLLARVGGNIEVLGFNARQRKAFLNAIMRWGMPPQDAFNSH  1450
1451  WLVRDLRGKSEKEFRAYVSLFMRHLCEPGADGAETFADGVPREGLSRQHV  1500
1501  LTRIGVMSLVRKKVQEFEHVNGKYSTPDLIPEGPEGKKSGEVISSDPNTP  1550
1551  VPASPAHLLPAPLGLPDKMEAQLGYMDEKDPGAQKPRQPLEVQALPAALD  1600
1601  RVESEDKHESPASKERAREERPEETEKAPPSPEQLPREEVLPEKEKILDK  1650
1651  LELSLIHSRGDSSELRPDDTKAEEKEPIETQQNGDKEEDDEGKKEDKKGK  1700
1701  FKFMFNIADGGFTELHTLWQNEERAAVSSGKIYDIWHRRHDYWLLAGIVT  1750
1751  HGYARWQDIQNDPRYMILNEPFKSEVHKGNYLEMKNKFLARRFKLLEQAL  1800
1801  VIEEQLRRAAYLNMTQDPNHPAMALNARLAEVECLAESHQHLSKESLAGN  1850
1851  KPANAVLHKVLNQLEELLSDMKADVTRLPSMLSRIPPVAARLQMSERSIL  1900
1901  SRLTNRAGDPTIQQGAFGSSQMYSNNFGPNFRGPGPGGIVNYNQMPLGPY  1950
1951  VTDI                                                1954

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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