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

NucPred

Fetching Q66JQ7 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MDGVYSEANEENDNTQRPVRRQHSSILKPPRSPLQDLKCGNQTNQEPNPP    50
  51  RKRKSSRRVSFADTIKVFQTESHMKTERNSEISGMNTLLCAPIQTQMQQK   100
 101  EFSITDCNHERKHANDQTVIFSDENQMDLTASHTVMITKGLSDCTKNENS   150
 151  TKIDTTSFLENLKHHAANSRIKKDLACSTVSLSQNIFSEKINSDNFIKRL   200
 201  KTGKHISSSTELDKENAEIPVYSKDSNSASSTYQMHASLGVDENSSNRTR   250
 251  IFREQDDGMNLTQCHTACIKTWIPPSTEAKIGEFKGDKTIYGNECMELTT   300
 301  NYTIQVLSSENNLSERETQTQNGMNVTTVDGATAPAPEKKTALKDKLNAA   350
 351  FQGSFPNPENKIHIIKCHPIESETHTVTQISSQSASTLAVTSKSICSSPA   400
 401  IEGYKTIFHSSSNDAMELTKCLSAMEEEKKLLKADDKYSKICTNPDAGPL   450
 451  REKTIYLEEDSMDITKSHTVAIDNKIFKHDQENIKKEIIAIPIFEKEMVL   500
 501  RNLMPMSKDEKRDVNYISVPQVSKESLQRSQTNTLSVSLTDKKMEFLADE   550
 551  DMDLTKSHTTKLSQVIPTTFDLASKNVTKSYSHSKSPLNEWESLDKQVVL   600
 601  GQHSKLPLPQRKDRDDPDCSHHKIMYSEELQTMDLTKSHTIVIGFGPSEV   650
 651  QEHSKINLEHKNSQLTAESIQTAVNVPAANSRVVTTNDMDMLKDRSTHKP   700
 701  ELLKEKQNIKIYGRKSIGRLKIDKTILFSEGNEGDMDITKSCTVKINHRS   750
 751  LLDKHDSHLVSLAGTSKTILHARGQVEMEINRSHTTPLECKIISPSDITP   800
 801  GDLDKTMMSIDDHEELDMTKSHTVFIDYQAEAKGVLPDRLDFQLSKKESL   850
 851  QKPKVTSLAEEIYISKNSESNHLPAKGSQLTILEEGSNSGLGEETNDAQK   900
 901  PGFLNELLSGKTQRRKSLSLKNKSITFPENDKSYREIPQSSAVEINNETR   950
 951  LEDRKGFSFVPLAGTSKPVLSAYGPEDMEISIGQTTASEYKTVPPEEITT  1000
1001  IPMDKTVMFVDNFGDLDVTRSHTVFIDCQAKEKVLDEYTNLGIQKTKTLS  1050
1051  GSEGDTHIQEITKNPAAQHKHHMTTVIPSSTVVSDQSSMKIKFHKADRDE  1100
1101  EVKGKEVEANMLKQTKPESCLLNITDGKNVDFTSSYTADVCRSSDKYSSL  1150
1151  PNISSSDNSGGNTMSLCDKNKEKAYNCQVPNEFTYAAILPSTYHMDSKKL  1200
1201  SVFPPCPSKEVTQTESAIALLKDEDPVEEPLGEMATFNSKHVSLNLAKDQ  1250
1251  TEAFVDVSVASQPHLSAQQSPSTQKGQDVARRDEGILAKAGKKALPFLLE  1300
1301  NVAASTWENESKIPTNVEHFAVTYEKELSISIQTDKCNTNVQSPSNSALT  1350
1351  TQVIQTHANAEGALDFLVPSTVSCFSSTKPSLSNLNRKTEEVLDFQTVNL  1400
1401  LPPAEQLLEEGSQAHSMSIVQATEIYRLGSRNDRDEESKTFCNEAETTSV  1450
1451  PLKTAVKDKTRRCSLGIFLPKLPSKRSCSITGVDDLEQILADAADLTQLE  1500
1501  TQPVCSKDPGIGSVAAKLNLSPSQFINEENLPVYPGEILSSDSVSLDIEE  1550
1551  SVLIDTSQRESLPSENKTENCRAQKRTRVEENDVTNEKKIRTHDSAQDQE  1600
1601  IFDNHMEEDINKNVNSVLLKSLSRTPSSCSSSLDSIKSDGLSLDVSTQRN  1650
1651  SQMESQFLGDTISEESLKEKLKDGQITIKEFFILLQVHILIQKPRQSTLP  1700
1701  AKFTINTLPTTEDLMLRQYVYGPRIQIYKEDCELLRQKIDELKISALNQN  1750
1751  KLLADVNRNLWEKVKDYSDEELKNYGIYLNKIKSRYTKMTKVFNHQGKVA  1800
1801  LYNKLVHSAENEKNKLQIKINEMDTILKKINNCLAEVETETKNLENEEKN  1850
1851  DAMEEWDSEMRDAEKELEQLKTEEEELQRKFLEVETQKTQTLAQIEFIKE  1900
1901  QTTKTEELLDQLSLSEWDVIEWSDDQAVFTFVYDSIELIITFGEPLVGLP  1950
1951  FLDKACRKINALSFQSLLDEDKAPPSSLLVHKLIFQYIEEQESWKKKCTA  2000
2001  QHQVPQMLQELSLVVNHCRLLGEEIEFLKRWGPNYSLMHINVNNTELRLL  2050
2051  FSSCAAFAKFEITLSPSAHYPLVPLPFTIHNHIGKTGHDEIAAIISKVPL  2100
2101  EENYLKNVVKQIYQDLLKD                                 2119

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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