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

NucPred

Fetching Q6P5D4 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MTTAAERKYINIRKRLDQLGYRQTLSVDSLPLVEKLFSDLVHTTESLRQC    50
  51  RLSSGKAEKESANLDFVLEPYKLENTRLNKENNELYLELMKLRECSDKHI   100
 101  KDLKTTLKKCSRETADLKFLNNQYVHKVKVLEKESKAKDEKIQQLQEKNL   150
 151  RAVVQTPGGRKRNIAFRRQRMQIDEPAPPSEVSAYPVPQPEDPYIADLLQ   200
 201  VADNRIQELQEEVQQLQEKLAQMEKGVLDYSKQIELREREIQRLSLALDG   250
 251  GCSPDVLSLETRNKTNEKLIAHLNVQVDFLQQANKELEKHIQELMETKET   300
 301  VTTEVVNLSNRNEKLCQELTEIDQLAQRLERHKEQVLETADKELGEAKKE   350
 351  IKRNLCEMRNLEEKMSKLQWELDLSHKEKERLNSELLLKSDLETVVHQLE   400
 401  QEKQRLSKKLQSFAVTERELTLEVERMRLEHGIKRRDKSPSRLDTFLKGI   450
 451  EEERDYYKKELEKLQHLIQRRSCAINYSAREKPPVVKCSEKGDCSTDVHL   500
 501  ITRERDELQRMLERFEKYMEDIQSNVKLLTAERDKLNVLYKEAKEELSTL   550
 551  RKESTNSTSPNHLVSCVEKEKERALSELRRITAEKEALREKLKNIQERNA   600
 601  VGKSDLEKTIEHLTYINHQLENEKYELQSKMLMMKETVESLENKSKLQAQ   650
 651  KLSHVTGDSSHQKTEMTSLRIVSEQLQRSLDDCQHRLSIKRGELESAQEQ   700
 701  IKMLEQKLENLSHRMTVQSEETHAMKKTIGVMDKEKDFLQETVDEKTEKI   750
 751  ANLQESLLSKEKVIAQLKVTVAEYETSLNQLQETLTTRDREINSLRRQLD   800
 801  ASHKELDDVGKSREISFKENRRLQDDLATMARENQEISLELEAAVQEKEE   850
 851  MKSRVHKYITEVSRWESLMAAKEKENKDLLDRFQMLHSRAEDWEVKAQQA   900
 901  EGENSSVRLELLSIDTERRHLRERVDLLEKEIQEHINAHHAYESQISSMA   950
 951  KAMSQLEEELRRHESEKATMLGDVSSLRELCIKLDSGKDVMTQQLNSKSL  1000
1001  ELERAVAELENVKSESELLKKQLTNERQTIKNLESLLATNRDKEFQSHLT  1050
1051  SHEKDTEIQLLKEKLNLSESKLTTQSRETSMLRTKVTQLQTDYDNLKRQM  1100
1101  SNEKYERERAIQEMRRLGLPTSPLSSTLKSPVQTPDHINA            1140

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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