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

NucPred

Fetching Q9DE46 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MSDSGSFAASRSRREKTEKSGRKEALERLKRAKAGEKVKYEVEQVSSIYE    50
  51  EVDEAEYSKLVRDRQDDDWIVDDDGTGYVEDGREIFDDDLEDNALADSGK   100
 101  GAKGAPKDKTNVKKSSVSKPNNIKSMFMASAVKKTTDKAVDLSKDDLLGD   150
 151  LLQDLKSQAVPITPPPVITLKKKKLAGSPLNPFSVPPTAPKVLPTSVKRL   200
 201  PAVTKPGHPAAQSKASVPRQIKKEPKAELISSAVGPLKVEAQVKEEDSGM   250
 251  VEFDDGDFDEPMEEDVEITPVDSSTIKTQAQSIKCVKEENIKEEKSSFIT   300
 301  SATLNESCWDQIDEAEPMTTEIQVDSSHLPLVTGADGSQVFRFYWLDAYE   350
 351  DQYSQPGVVYLFGKVWIESADAYVSCCVSVKNIERTVYLLPRENRVQLST   400
 401  GKDTGAPVSMMHVYQEFNEAVAEKYKIMKFKSKKVDKDYAFEIPDVPASS   450
 451  EYLEVRYSADSPQLPQDLKGETFSHVFGTNTSSLELFLLSRKIKGPSWLE   500
 501  IKSPQLSSQPMSWCKVEAVVTRPDQVSVVKDLAPPPVVVLSLSMKTVQNA   550
 551  KTHQNEIVAIAALVHHTFPLDKAPPQPPFQTHFCVLSKLNDCIFPYDYNE   600
 601  AVKQKNANIEIALTERTLLGFFLAKIHKIDPDVIVGHDIYGFDLEVLLQR   650
 651  INSCKVPFWSKIGRLRRSVMPKLGGRSGFAERNAACGRIICDIEISAKEL   700
 701  IRCKSYHLSELVHQILKAERVVIPPENIRNAYNDSVHLLYMLENTWIDAK   750
 751  FILQIMCELNVLPLALQITNIAGNVMSRTLMGGRSERNEYLLLHAFTENN   800
 801  FIVPDKPVFKKMQQTTVEDNDDMGTDQNKNKSRKKAAYAGGLVLEPKVGF   850
 851  YDKFILLLDFNSLYPSIIQEYNICFTTVHREAPSTQKGEDQDEIPELPHS   900
 901  DLEMGILPREIRKLVERRRHVKQLMKQPDLNPDLYLQYDIRQKALKLTAN   950
 951  SMYGCLGFSYSRFYAKPLAALVTHQGREILLHTKEMVQKMNLEVIYGDTD  1000
1001  SIMINTNCNNLEEVFKLGNRVKSEINKSYKLLEIDIDGIFKSLLLLKKKK  1050
1051  YAALTVEPTGDGKYVTKQELKGLDIVRRDWCELAKQAGNYVISQILSDQP  1100
1101  RDSIVENIQKKLTEIGENVTNGTVPITQYEINKALTKDPQDYPDKKSLPH  1150
1151  VHVALWINSQGGRKVKAGDTISYVICQDGSNLSASQRAYAQEQLQKQENL  1200
1201  SIDTQYYLSQQVHPVVARICEPIDGIDSALIAMWLGLDPSQFRAHRHYQQ  1250
1251  DEENDALLGGPSQLTDEEKYRDCERFKFFCPKCGTENIYDNVFDGSGLQI  1300
1301  EPGLKRCSKPECDASPLDYVIQVHNKLLLDIRRYIKKYYSGWLVCEEKTC  1350
1351  QNRTRRLPLSFSRNGPICQACSKATLRSEYPEKALYTQLCFYRFIFDWDY  1400
1401  ALEKVVSEQERGHLKKKLFQESENQYKKLKSTVDQVLSRSGYSEVNLSKL  1450
1451  FQTLNTIK                                            1458

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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