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

NucPred

Fetching P53565 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MAANVGSMFQYWKRFDLQQLQRELDATATVLANRQDESEQSRKRLIEQSR    50
  51  EFKKNTPEDLRKQVAPLLKSFQGEIDALSKRSKEAEAAFLTVYKRLIDVP   100
 101  DPVPALDLGQQLEIKVQRLHDIETENQKLRETLEEYNKEFAEVKNQEVTI   150
 151  KALKEKIREYEQTLKSQAETIALEKEQKLQNDFAEKERKLQETQMSTTSK   200
 201  LEEAEHKLQTLQTALEKTRTELFDLKTKYDEETTAKADEIEMIMTDLERA   250
 251  NQRAEVAQREAETLREQLSSANHSLQLASQIQKAPDVAIEVLTRSSLEVE   300
 301  LAAKEREIAQLVEDVQRLQASLTKLRENSASQISQLEQQLNAKNSTLKQL   350
 351  EEKLKGQADYEDVKKELTTLKSMEFAPSEGAGTQDSTKPLEVLLLEKNRS   400
 401  LQSENATLRISNSDLSGSARRKGRDQPESRRPGPLPASPPPQLPRNTGEQ   450
 451  VSNTNGTHHFSPAGLSQDFFSSNLASPSLPLASTGKFALNSLLQRQLMQS   500
 501  FYSKAMQEAGSTSTIFSTGPYSTNSISSPSPLQQSPDVNGMAPSPSQSES   550
 551  AGSISEGEEIDTAEIARQVKEQLIKHNIGQRIFGHYVLGLSQGSVSEILA   600
 601  RPKPWNKLTVRGKEPFHKMKQFLSDEQNILALRSIQGRQRGNITTRIRAS   650
 651  ETGSDEAIKSILEQAKRELQVQKTAEPVQASSTASSGNSDDAIRSILQQA   700
 701  RREMEAQQAALDPALKPAPLSQPDLTILNPKLLSASPMSTVSTYPPLAIS   750
 751  LKKTPAAPEASTSALPSAPALKKEAQDAPTLDPPGSADATPGVLRPVKNE   800
 801  LVRGSTWKDPWWNPVQPERRNLTTSEETKADETNASGKEKTGSSQPRAER   850
 851  SQLQGPSATAEYWKEWPNAESPYSQSSELSLTGASRSETPQNSPLPSSPI   900
 901  VPMAKPAKPSVPPLTPEQYEVYMYQEVDTIELTRQVKEKLAKNGICQRIF   950
 951  GEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFIRMQLWLNGELGQGVLP  1000
1001  VQGQQQGPVLHSVTSLQDPLQQGCVSSESTPKTSASCSPAPESPMSSSES  1050
1051  VKSLTELVQQPCPTIETSKEGKPPEPSDPPTSDSQPTTPLPLSGHSALSI  1100
1101  QELVAMSPELDTYGITKRVKEVLTDNNLGQRLFGETILGLTQGSVSDLLA  1150
1151  RPKPWHKLSLKGREPFVRMQLWLNDPNNVEKLMDMKRMEKKAYMKRRHSS  1200
1201  VSDSQPCEPPSVGIDYSQGASPQPQHQLKKPRVVLAPEEKEALKRAYQQK  1250
1251  PYPSPKTIEELATQLNLKTSTVINWFHNYRSRIRRELFIEEIQAGSQGQA  1300
1301  GASDSPSARSSRAAPSSEGDSCDGVEAADTEEPGGNIVATKSQGGPAEVT  1350
1351  AAPADREEATQPAEKAKAQPLSSGTPGQDDGEDAGRSRPPPEGLADAPAP  1400
1401  VPNLAAPAAGEDAATSATAPAMATEAPGAARAGPAERSSALPSTSAPANA  1450
1451  PARRPSSLQSLFGLPEAAGARDNPVRKKKAANLNSIIHRLEKAASREEPI  1500
1501  EWEF                                                1504

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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