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

NucPred

Fetching P83510 from www.uniprot.org...

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

   1  MASDSPARSLDEIDLSALRDPAGIFELVELVGNGTYGQVYKGRHVKTGQL    50
  51  AAIKVMDVTGDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKNPPGMDDQ   100
 101  LWLVMEFCGAGSVTDLIKNTKGNTLKEEWIAYICREILRGLSHLHQHKVI   150
 151  HRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVI   200
 201  ACDENPDATYDFKSDLWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPA   250
 251  PRLKSKKWSKKFQSFIESCLVKNHSQRPATEQLMKHPFIRDQPNERQVRI   300
 301  QLKDHIDRTKKKRGEKDETEYEYSGSEEEEEENDSGEPSSILNLPGESTL   350
 351  RRDFLRLQLANKERSEALRRQQLEQQQRENEEHKRQLLAERQKRIEEQKE   400
 401  QRRRLEEQQRREKELRKQQEREQRRHYEEQMRREEERRRAEHEQEYKRKQ   450
 451  LEEQRQAERLQRQLKQERDYLVSLQHQRQEQRPLEKKPLYHYKEGMSPSE   500
 501  KPAWAKEVEERSRLNRQSSPAMPHKVANRISDPNLPPRSESFSISGVQPA   550
 551  RTPPMLRPVDPQIPQLVAVKSQGPALTASQSVHEQPTKGLSGFQEALNVT   600
 601  SHRVEMPRQNSDPTSENPPLPTRIEKFDRSSWLRQEEDIPPKVPQRTTSI   650
 651  SPALARKNSPGNGSALGPRLGSQPIRASNPDLRRTEPVLESSLQRTSSGS   700
 701  SSSSSTPSSQPSSQGGSQPGSQAGSSERSRVRANSKSEGSPVLPHEPSKV   750
 751  KPEESRDITRPSRPADLTALAKELRELRIEETNRPLKKVTDYSSSSEESE   800
 801  SSEEEEEDGESETHDGTVAVSDIPRLIPTGAPGNNEQYNMGMVGTHGLET   850
 851  SHADTFGGSISREGTLMIRETAEEKKRSGHSDSNGFAGHINLPDLVQQSH   900
 901  SPAGTPTEGLGRVSTHSQEMDSGAEYGIGSSTKASFTPFVDPRVYQTSPT   950
 951  DEDEEDDESSAAALFTSELLRQEQAKLNEARKISVVNVNPTNIRPHSDTP  1000
1001  EIRKYKKRFNSEILCAALWGVNLLVGTENGLMLLDRSGQGKVYNLINRRR  1050
1051  FQQMDVLEGLNVLVTISGKKNKLRVYYLSWLRNRILHNDPEVEKKQGWIT  1100
1101  VGDLEGCIHYKVVKYERIKFLVIALKNAVEIYAWAPKPYHKFMAFKSFAD  1150
1151  LQHKPLLVDLTVEEGQRLKVIFGSHTGFHVIDVDSGNSYDIYIPSHIQGN  1200
1201  ITPHAIVILPKTDGMEMLVCYEDEGVYVNTYGRITKDVVLQWGEMPTSVA  1250
1251  YIHSNQIMGWGEKAIEIRSVETGHLDGVFMHKRAQRLKFLCERNDKVFFA  1300
1301  SVRSGGSSQVFFMTLNRNSMMNW                             1323

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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