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

NucPred

Fetching Q8R311 from www.uniprot.org...

The NucPred score for your sequence is 0.67 (see score help below)

   1  MAEVSVQRILLLVVSLAKCLEGTKLLAHLKKCGDLECETLISRVLALRDY    50
  51  TGPDCRYLNFTTGEEISVYVKLGGDREDLWAGSKGKDFGFFPRDAVEIEE   100
 101  VFISEEVEMPTKSDFLCLLGEGYIFGSEQSELNSEDDEEHMYPYEKDEDQ   150
 151  NYNIYEGDFQPEPDLYAAAEGTLLEDQIPASEAPDDFRFSSEWKAWEGAG   200
 201  SQGGGEQDYTADSDQDLPSLSKPERQGWFGLGTEEAEEKVFESDTEPTQE   250
 251  LALEEESDLEKLHSGEPQVELEQEPKSETLEFSSVPDEEYELESETESIL   300
 301  KPQASGWFGEGLTSYLGFGNEEAGLELLSKESNPPLQDIPSSVPPDEEVP   350
 351  APCREISTDKEDAVINDSSVLSPSWFYYGFGMLGFTNADEDNIVSDKGEN   400
 401  EDGEVDNLKHPIGSDFDPEKEQERKIVTVETEDQAGTESVLEKTDESGSM   450
 451  QYLKKFFDNPWGFQSLPEDTELPFSKKMLDQDDIVENDKIEELSTENSPT   500
 501  GSMKDPVMLASRYVLSDIDSEVELPMEEHEGVHFKPSSSKRNEDDSNSWA   550
 551  DPEELSVAQTDGSAEGALLDTQLVSPKEHAADFQLLKYLLQIDVYGFMSS   600
 601  ALSPIEILLESVVAALPEDMRADFNPSGFSLELAVCVLSVGLLAVVLFLW   650
 651  RGFRSIRSRFYVGREKKLALELSALIEEKCKLLDKVSIVQKEYEGLESSL   700
 701  KEASFEKESTEAQSLEFVEGSQISEATYENLEQSKSKLEDEILLLEEKLE   750
 751  EERAKHSEQDELMADISKRIQSLEDESKSLKSQVAEAKTTFRIFEINEER   800
 801  LKGAIKDALNENSQLQESQKQLLQETEMMKEQVNDLDKQKVALEESRAQA   850
 851  EQALSEKESQIETLVTSLLKMKDWAAVLGEADDGNLDLDMKSGLENTAAL   900
 901  DNQPKGALKKLIYAAKLNASLKALEGERNQVYTQLSEVDQVKEDLTEHIK   950
 951  SLESKQASLQSEKTEFESESQKLQQKLKVITELYQENEMKLHRKLTVEEN  1000
1001  YRLEKEEKLSKVDEKISHATEELETCRQRAKDLEEELERTIHSYQGQVIS  1050
1051  HEKKAHDNWLAARTLERNLNDLRKENAHNRQKLTETEFKFELLEKDPYAL  1100
1101  DVPNTAFGREHSPYGPSPLGRPPSETRAFLSPPTLLEGPLRLSPLLPGGG  1150
1151  GRGSRGPENLLDHQMNTERGESSYDRLSDAPRAPSDRSLSPPWEQDRRMT  1200
1201  AHPPPGQPYSDPALQRQDRFYPNSGRLSGPAELRSYNMPSLDKVDGPVPS  1250
1251  EMESSGNGTKDNLGNSNVPDSPIPAECEAAGRGFFPPPFPPVRDPLFPVD  1300
1301  PRSQFMRRGPSFPPPPPGSIYAAPRDYFPPRDFPGPPLPPFPGRTVYAPR  1350
1351  GFPPYLPPRAGFFPPPPHPESRSELPPDLIPPSKEPAADPPETQEA      1396

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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