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

NucPred

Fetching Q93971 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MMSDDMLDENDENFACQDVDEIIIYVPEFAGYREVNIDTAVSVCPTPIQQ    50
  51  ARRESSCRNLEMRRRFEKLRREKKEEKKLLADDEKDFDEDDDVFEDGEGL   100
 101  QMRTFQPNASIRDENGSMPSLLPRTAPIKKTRKHRRRRSGSFTGGVYPRK   150
 151  GHRNRSLLGHAIPPPNVHSADWRDMLAITDNKDDKLMKTLGVTRYLQSKG   200
 201  GDQVPPTSTTTGGAGGDGNAVPTTSQAQAQTFNSGRQTTGMSSGDRLNED   250
 251  VSATANSAQLVLPTPLFNQMRFTESNMSLNRHNWVRETFTRRECSRFIAS   300
 301  SRDLHKCGCGRTRDAHRNIPELTSEFLRQKRSVAALEQQRSISNVNDDIN   350
 351  TQNMYTKRGANEKWSLRKHTVSLATNAFGQVEFQGGPHPYKAQYVRVNFD   400
 401  TEPAYIMSLFEHVWQISPPRLIITVHGGTSNFDLQPKLARVFRKGLLKAA   450
 451  STTGAWIITSGCDTGVVKHVAAALEGAQSAQRNKIVCIGIAPWGLLKKRE   500
 501  DFIGQDKTVPYYPSSSKGRFTGLNNRHSYFLLVDNGTVGRYGAEVILRKR   550
 551  LEMYISQKQKIFGGTRSVPVVCVVLEGGSCTIRSVLDYVTNVPRVPVVVC   600
 601  DGSGRAADLLAFAHQNVTEDGLLPDDIRRQVLLLVETTFGCSEAAAHRLL   650
 651  HELTVCAQHKNLLTIFRLGEQGEHDVDHAILTALLKGQNLSAADQLALAL   700
 701  AWNRVDIARSDVFAMGHEWPQAALHNAMMEALIHDRVDFVRLLLEQGINM   750
 751  QKFLTISRLDELYNTDKGPPNTLFYIVRDVVRVRQGYRFKLPDIGLVIEK   800
 801  LMGNSYQCSYTTSEFRDKYKQRMKRVKHAQKKAMGVFSSRPSRTGSGIAS   850
 851  RQSTEGMGGVGGGSSVAGVFGNSFGNQDPPLDPHVNRSALSGSRALSNHI   900
 901  LWRSAFRGNFPANPMRPPNLGDSRDCGSEFDEELSLTSASDGSQTEPDFR   950
 951  YPYSELMIWAVLTKRQDMAMCMWQHGEEAMAKALVACRLYKSLATEAAED  1000
1001  YLEVEICEELKKYAEEFRILSLELLDHCYHVDDAQTLQLLTYELSNWSNE  1050
1051  TCLALAVIVNNKHFLAHPCCQILLADLWHGGLRMRTHSNIKVVLGLICPP  1100
1101  FIQMLEFKTREELLNQPQTAAEHQNDMNYSSSSSSSSSSSSSSSSSDSSS  1150
1151  FEDDDDENNAHNHDQKRTRKTSQGSAQSLNITSLFHSRRRKAKKNEKCDR  1200
1201  ETDASACEAGNRQIQNGGLTAEYGTFGESNGVSPPPPYMRANSRSRYNNR  1250
1251  SDMSKTSSVIFGSDPNLSKLQKSNITSTDRPNPMEQFQGTRKIKMRRRFY  1300
1301  EFYSAPISTFWSWTISFILFITFFTYTLLVKTPPRPTVIEYILIAYVAAF  1350
1351  GLEQVRKIIMSDAKPFYEKIRTYVCSFWNCVTILAIIFYIVGFFMRCFGS  1400
1401  VAYGRVILACDSVLWTMKLLDYMSVHPKLGPYVTMAGKMIQNMSYIIVML  1450
1451  VVTLLSFGLARQSITYPDETWHWILVRNIFLKPYFMLYGEVYADEIDTCG  1500
1501  DEAWDQHLENGGPVILGNGTTGLSCVPGYWIPPLLMTFFLLIANILLMSM  1550
1551  LIAIFNHIFDATDEMSQQIWLFQRYKQVMEYESTPFLPPPLTPLYHGVLI  1600
1601  LQFVRTRLSCSKSQERNPMFDFSLKLFLDNDQIEKLHDFEEDCMEDLARQ  1650
1651  KLNEKNTSNEQRILRADIRTDQILNRLIDLQAKESMGRDVINDVESRLAS  1700
1701  VEKAQNEILECVRALLNQNNAPTAIGRCFSPSPDPLVETANGTPGPLLLK  1750
1751  LPGTDPILEEKDHDSGENSNSLPPGRIRRNRTATICGGYVSEERNMMLLS  1800
1801  PKPSDVSGIPQQRLMSVTSMDPLPLPLAKLSTMSIRRRHEEYTSITDSIA  1850
1851  IRHPERRIRNNRSNSSEHDESAVDSEGGGNVTSSPRKRSTRDLRMTPSSQ  1900
1901  VEESTSRDQIFEIDHPEHEEDEAQADCELTDVITEEEDEEEDDEEDDSHE  1950
1951  RHHIHPRRKSSRQNRQPSHTLETDLSEGEEVDPLDVLKMKELPIIHQILN  2000
2001  EEEQAGAPHSTPVIASPSSSRADLTSQKCSDV                    2032

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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