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

NucPred

Fetching Q8IXJ9 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MKDKQKKKKERTWAEAARLVLENYSDAPMTPKQILQVIEAEGLKEMRSGT    50
  51  SPLACLNAMLHSNSRGGEGLFYKLPGRISLFTLKKDALQWSRHPATVEGE   100
 101  EPEDTADVESCGSNEASTVSGENDVSLDETSSNASCSTESQSRPLSNPRD   150
 151  SYRASSQANKQKKKTGVMLPRVVLTPLKVNGAHVESASGFSGCHADGESG   200
 201  SPSSSSSGSLALGSAAIRGQAEVTQDPAPLLRGFRKPATGQMKRNRGEEI   250
 251  DFETPGSILVNTNLRALINSRTFHALPSHFQQQLLFLLPEVDRQVGTDGL   300
 301  LRLSSSALNNEFFTHAAQSWRERLADGEFTHEMQVRIRQEMEKEKKVEQW   350
 351  KEKFFEDYYGQKLGLTKEESLQQNVGQEEAEIKSGLCVPGESVRIQRGPA   400
 401  TRQRDGHFKKRSRPDLRTRARRNLYKKQESEQAGVAKDAKSVASDVPLYK   450
 451  DGEAKTDPAGLSSPHLPGTSSAAPDLEGPEFPVESVASRIQAEPDNLARA   500
 501  SASPDRIPSLPQETVDQEPKDQKRKSFEQAASASFPEKKPRLEDRQSFRN   550
 551  TIESVHTEKPQPTKEEPKVPPIRIQLSRIKPPWVVKGQPTYQICPRIIPT   600
 601  TESSCRGWTGARTLADIKARALQVRGARGHHCHREAATTAIGGGGGPGGG   650
 651  GGGATDEGGGRGSSSGDGGEACGHPEPRGGPSTPGKCTSDLQRTQLLPPY   700
 701  PLNGEHTQAGTAMSRARREDLPSLRKEESCLLQRATVGLTDGLGDASQLP   750
 751  VAPTGDQPCQALPLLSSQTSVAERLVEQPQLHPDVRTECESGTTSWESDD   800
 801  EEQGPTVPADNGPIPSLVGDDTLEKGTGQALDSHPTMKDPVNVTPSSTPE   850
 851  SSPTDCLQNRAFDDELGLGGSCPPMRESDTRQENLKTKALVSNSSLHWIP   900
 901  IPSNDEVVKQPKPESREHIPSVEPQVGEEWEKAAPTPPALPGDLTAEEGL   950
 951  DPLDSLTSLWTVPSRGGSDSNGSYCQQVDIEKLKINGDSEALSPHGESTD  1000
1001  TASDFEGHLTEDSSEADTREAAVTKGSSVDKDEKPNWNQSAPLSKVNGDM  1050
1051  RLVTRTDGMVAPQSWVSRVCAVRQKIPDSLLLASTEYQPRAVCLSMPGSS  1100
1101  VEATNPLVMQLLQGSLPLEKVLPPAHDDSMSESPQVPLTKDQSHGSLRMG  1150
1151  SLHGLGKNSGMVDGSSPSSLRALKEPLLPDSCETGTGLARIEATQAPGAP  1200
1201  QKNCKAVPSFDSLHPVTNPITSSRKLEEMDSKEQFSSFSCEDQKEVRAMS  1250
1251  QDSNSNAAPGKSPGDLTTSRTPRFSSPNVISFGPEQTGRALGDQSNVTGQ  1300
1301  GKKLFGSGNVAATLQRPRPADPMPLPAEIPPVFPSGKLGPSTNSMSGGVQ  1350
1351  TPREDWAPKPHAFVGSVKNEKTFVGGPLKANAENRKATGHSPLELVGHLE  1400
1401  GMPFVMDLPFWKLPREPGKGLSEPLEPSSLPSQLSIKQAFYGKLSKLQLS  1450
1451  STSFNYSSSSPTFPKGLAGSVVQLSHKANFGASHSASLSLQMFTDSSTVE  1500
1501  SISLQCACSLKAMIMCQGCGAFCHDDCIGPSKLCVLCLVVR           1541

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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