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

NucPred

Fetching Q6T4R5 from www.uniprot.org...

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

   1  MPFAKRIVEPQWLCRQRRPAPGPAVDASGGSAEPPPPLQPPGRRDLDEVE    50
  51  APGPEEPARAVPAPSGLPPPPPPLPAPADQTQPPHGEASVAGEESTAGIP   100
 101  EAAPAAGEASSAAAAAAVLLMLDLCAVSNAALARVLRQLSDVARHACSLF   150
 151  QELESDIQLTHRRVWALQGKLGGVQRVLSTLDPKQEAVPVSNLDIESKLS   200
 201  VYYRAPWHQQRNIFLPATRPPCVEELHRHARQSLQALRREHRSRSDRREQ   250
 251  RAAAPLSIAAPPLPAYPPAHSQRRREFKDRHFLTFNSTRSPSPTECCHMT   300
 301  PWSRKSHPPEDEDTDVMLGQRPKNPIHNIPSTLDKQTNWSKALPLPTPEE   350
 351  KMKQDAQVISSCIIPINVTGVGFDREASIRCSLVHSQSVLQRRRKLRRRK   400
 401  TISGIPRRVQQEIDSDESPVARERNVIVHTNPDPSNTVNRISGTRDSECQ   450
 451  TEDILIAAPSRRRIRAQRGQSIAASLSHSAGNISALADKGDTMFTPAVSS   500
 501  RTRSRSLPREGNRGGDAEPKVGAKPSAYEEGESFVGDHERTPNDFSEAPS   550
 551  SPSAQDHQPTLGLACSQHLHSPQHKLSERGRSRLSRMAADSGSCDISSNS   600
 601  DTFGSPIHCISTAGVLLSSHMDQKDDHQSSSGNWSGSSSTCPSQTSETIP   650
 651  PAASPPLTGSSHCDSELSLNTAPHANEDASVFVTEQYNDHLDKVRGHRAN   700
 701  SFTSTVADLLDDPNNSNTSDSEWNYLHHHHDASCRQDFSPERPKADSLGC   750
 751  PSFTSMATYDSFLEKSPSDKADTSSHFSVDTEGYYTSMHFDCGLKGNKSY   800
 801  VCHYAALGPENGQGVGASPGLPDCAWQDYLDHKRQGRPSISFRKPKAKPT   850
 851  PPKRSSSLRKSDGNADISEKKEPKISSGQHLPHSSREMKLPLDFANTPSR   900
 901  MENANLPTKQEPSWINQSEQGIKEPQLDASDIPPFKDEVAESTHYADLWL   950
 951  LNDLKTNDPYRSLSNSSTATGTTVIECIKSPESSESQTSQSESRATTPSL  1000
1001  PSVDNEFKLASPEKLAGLASPSSGYSSQSETPTSSFPTAFFSGPLSPGGS  1050
1051  KRKPKVPERKSSLQQPSLKDGTISLSKDLELPIIPPTHLDLSALHNVLNK  1100
1101  PFHHRHPLHVFTHNKQNTVGETLRSNPPPSLAITPTILKSVNLRSINKSE  1150
1151  EVKQKEENNTDLPYLEESTLTTAALSPSKIRPHTANKSVSRQYSTEDTIL  1200
1201  SFLDSSAVEMGPDKLHLEKNSTFDVKNRCDPETITSAGSSLLDSNVTKDQ  1250
1251  VRTETEPIPENTPTKNCAFPTEGFQRVSAARPNDLDGKIIQYGPGPDETL  1300
1301  EQVQKAPSAGLEEVAQPESVDVITSQSDSPTRATDVSNQFKHQFVMSRHH  1350
1351  DKVPGTISYESEITSVNSFPEKCSKQENIASGISAKSASDNSKAEETQGN  1400
1401  VDEASLKESSPSDDSIISPLSEDSQAEAEGVFVSPNKPRTTEDLFAVIHR  1450
1451  SKRKVLGRKDSGDMSVRSKSRAPLSSSSSSASSITSPSSNVTTPNSQRSP  1500
1501  GLIYRNAKKSNTSNEEFKLLLLKKGSRSDSSYRMSATEILKSPILPKPPG  1550
1551  ELTAESPQSTDDAHQGSQGAEALSPLSPCSPRVNAEGFSSKSFATSASAR  1600
1601  VGRSRAPPAASSSRYSVRCRLYNTPMQAISEGETENSDGSPHDDRSSQSS  1650
1651  T                                                   1651

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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