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

NucPred

Fetching Q27746 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MPSKTICDQVIPPNVRDRVQELDGDLNDGLITEKGYVKKKSKILFEHLSP    50
  51  DIQTKLKGLEDELKDEELTEKGYLNKVQSILAKFIETCSPVNGDTKEEAS   100
 101  SNGKDDEKAESTVANGTTSNGSTTNGSSGSSKANGHTNGGYVQSSSQEET   150
 151  GTSQSEEEMDMDTPTSGKGGSKKKKKSKGSGGGDAGKGRKRKVLGDDERD   200
 201  GVEKKEGEKKDVEGEEGEEAKEESATPDEKTLRTSKRKRSPKADAKQPSI   250
 251  MSMFTKKPAKKEEEKMEESSSMEVDKKEMENGDNGKKEEEEPSGPGGKRI   300
 301  KKEEEEEEKAKVEPMSPSRDLRHKANHETAESKQPPLRCKECRQLLDDPD   350
 351  LKIFPGDPEDAREEYITLTDPRLSLLTGDEGDAMSYDERLQHKITNFCVY   400
 401  DKSTHICAFDRGMIEKNKELYFSGYVKPIYDDNPSTEGGIPTKRIGPINE   450
 451  WYTTGFDGGHKALIGFSTAFAEYIVMSPSEEYKPFWTAVQEKIYMSKILI   500
 501  EFLQNNVDPVYEDLLTQIETTVPPEGCNRFTEDSLLRHAQFVVEQVESYD   550
 551  DAADRDEVLLITMPCMRDLIKLAGVTLGKRRAARKAAAVKKDKKPVFTMA   600
 601  TVTPLVSHIFDAIFKDQIADEMKAAASERKKRCGVCEICQAPDCGKCTAC   650
 651  KDMIKFGGSGKAKQACKDRRCPNMAVQEADENDIDEMDNSSNKENKDEKK   700
 701  AKKGRKLETPLKKKKRAKVTWLDEPTEVTEERAYYKAAMLDDEKIEIGDC   750
 751  VLIHPDDPTKPLFMARVIYMWQESQGEMMFHAQWFVYGSETVLGETSDPL   800
 801  EVFPIDECQDTYLGSVNAKCTVIYKAPPNDWSMIGGIDDPETDHVIKEDD   850
 851  GKTFFYQKWYDPELARFEDYEVLMAPDDIPAHRFCSCCLKNERAQEKETA   900
 901  RPGAKLEDQDDSSKVLYSSWHYKGNEFQIGDGVYLLPEVFSFNIKQKVVT   950
 951  KKPVSKKDVDEDLYPENYRKSSEYVKGSNLECPEPFRIGKIISIYTTKSN  1000
1001  STVRLRVNKMYRPEDTHKGRTAAYQADLNVLYWSEEEAVTELEVVQGKCS  1050
1051  VVCAEDLNVSTDEYSAGGPHKFYFREAYDSERKCFEDPPSKSRSTRMKGK  1100
1101  GKGKGKGKAKGKIAVEKEEEKESTETPFNKLKCLDVFAGCGGLSEGFHQA  1150
1151  GICESSWAIEKEEPAAQAYRLNNPGSTVFSDDCNELLRLVMQGEKTSRTG  1200
1201  QKLPQKGDVELLCGGPPCQGFSGMNRFNSREYSKFKNSLISSYLSYCDYY  1250
1251  RPRFFLLENVRNFVSYKKNMVLKLALRCLIRMGYQCTFGILQAGQYGVPQ  1300
1301  TRRRAIILAAAPGEKLPFYPEPLHVFSSRACSLSVMIGEKKIESNNQWCL  1350
1351  SAPYRTITVRDTMSDLPTINNGAQKLEISYDGEPQSDFQKKIRGNQYQPI  1400
1401  LRDHICKDMSSLVAARMKHIPLAPGSDWRDLPNIPVTLKDGTTCRKLRYT  1450
1451  HKDKKNGKSSTGALRGVCSCAEGDACDPSDRQFSTLIPWCLPHTGNRHNN  1500
1501  WAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGF  1550
1551  PDTYRFFGSILDKHRQIGNAVPPPMAAAIGMEIKVCLQTKTKRDQERAAL  1600
1601  EPVKEETEESMD                                        1612

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.)

Go back to the NucPred Home Page.