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

NucPred

Fetching Q91YD4 from www.uniprot.org...

The NucPred score for your sequence is 0.61 (see score help below)

   1  MESLDRRRTGSEQEEGFGVQSRRATDLGMVPNLRRSNSSLCKSRRFLCSF    50
  51  SSEKQENLSSWIPENIKKKECVYFVESSKLSDAGKVVCACGYTHEQHLEV   100
 101  AIKPHTFQGKEWDPKKHVQEMPTDAFGDIVFTDLSQKVGKYVRVSQDTPS   150
 151  SVIYQLMTQHWGLDVPNLLISVTGGAKNFNMKLRLKSIFRRGLVKVAQTT   200
 201  GAWIITGGSHTGVMKQVGEAVRDFSLSSSCKEGEVITIGVATWGTIHNRE   250
 251  GLIHPMGGFPAEYMLDEEGQGNLTCLDSNHSHFILVDDGTHGQYGVEIPL   300
 301  RTKLEKFISEQTKERGGVAIKIPIVCVVLEGGPGTLHTIYNAINNGTPCV   350
 351  IVEGSGRVADVIAQVATLPVSEITISLIQQKLSIFFQEMFETFTENQIVE   400
 401  WTKKIQDIVRRRQLLTIFREGKDGQQDVDVAILQALLKASRSQDHFGHEN   450
 451  WDHQLKLAVAWNRVDIARSEIFTDEWQWKPADLHPMMTAALISNKPEFVR   500
 501  LFLENGVRLKEFVTWDTLLCLYENLEPSCLFHSKLQKVLAEEQRLAYASA   550
 551  TPRLHMHHVAQVLRELLGDSTQLLYPRPRYTDRPRLSMTVPHIKLNVQGV   600
 601  SLRSLYKRSTGHVTFTIDPVRDLLIWAVIQNHRELAGIIWAQSQDCTAAA   650
 651  LACSKILKELSKEEEDTDSSEEMLALADEFEHRAIGVFTECYRKDEERAQ   700
 701  KLLVRVSEAWGKTTCLQLALEAKDMKFVSHGGIQAFLTKVWWGQLCVDNG   750
 751  LWRIILCMLAFPLLFTGFISFREKRLQALCRPARVRAFFNAPVVIFHMNI   800
 801  LSYFAFLCLFAYVLMVDFQPSPSWCEYLIYLWLFSLVCEETRQLFYDPDG   850
 851  CGLMKMASLYFSDFWNKLDVGAILLFIVGLTCRLIPATLYPGRIILSLDF   900
 901  IMFCLRLMHIFTISKTLGPKIIIVKRMMKDVFFFLFLLAVWVVSFGVAKQ   950
 951  AILIHNESRVDWIFRGVVYHSYLTIFGQIPTYIDGVNFSMDQCSPNGTDP  1000
1001  YKPKCPESDWTGQAPAFPEWLTVTLLCLYLLFANILLLNLLIAMFNYTFQ  1050
1051  EVQEHTDQIWKFQRHDLIEEYHGRPPAPPPLILLSHLQLLIKRIVLKIPA  1100
1101  KRHKQLKNKLEKNEETALLSWELYLKENYLQNQQYQQKQRPEQKIQDISE  1150
1151  KVDTMVDLLDMDQVKRSGSTEQRLASLEEQVTQVTRALHWIVTTLKDSGF  1200
1201  GSGAGALTLAPQRAFDEPDAELSIRRKVEEPGDGYHVSARHLLYPNARIM  1250
1251  RFPVPNEKVPWAAEFLIYDPPFYTAEKDVALTDPVGDTAEPLSKISYNVV  1300
1301  DGPTDRRSFHGVYVVEYGFPLNPMGRTGLRGRGSLSWFGPNHTLQPVVTR  1350
1351  WKRNQGGAICRKSVRKMLEVLVMKLPRSEHWALPGGSREPGEMLPRKLKR  1400
1401  VLRQEFWVAFETLLMQGTEVYKGYVDDPRNTDNAWIETVAVSIHFQDQND  1450
1451  MELKRLEENLHTHDPKELTRDLKLSTEWQVVDRRIPLYANHKTILQKVAS  1500
1501  LFGAHF                                              1506

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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