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

NucPred

Fetching Q9I7F7 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MEYPQIDLYEFLTESELQQYYNAVKNELKITNAAQFKYAADEDLRFIGLS    50
  51  RPEIRRLRKFYEKHFPHSYLSKIKRLLQAPGTMVKREEAPGGGSQVALDG   100
 101  SSASACSSLAAKNGASSPSKVPNNKHIIPADSISVNKQLGTGEFGIVQQG   150
 151  VWSNGNERIQVAIKCLCRERMQSNPMEFLKEAAIMHSIEHENIVRLYGVV   200
 201  LATDSLMLVTELAHLRSLLECLKDSGLRVSFLTIPTLCEFALQICNGMRY   250
 251  LEQKRLIHRDLAARNILVFSKDKVKISDFGLSRALGVGKDYYKTNFNVNL   300
 301  KLPIAWCAPECINYLRFTNASDVWAFGVCLWEMFSYGFQPWAALTGLQIL   350
 351  EAIDAPNYQRLEQPDCCPSEYYTLMMKCWQDDAAKRPRFGEIYDQLPDMK   400
 401  PEQLKAVVNCTEPKKDHLLYRQGDIISVLDRNTGTPFWKGVLSTGKTGYF   450
 451  NPSNTVAFLEGLPSSTRDSFSRVSDHRISKRKLRTEMISKPQNDFKHTGH   500
 501  VGIDGATFGDIAFLGSSQNYNHVPKQIVTPYKPSEDIEQTPLLLPPTPTS   550
 551  PDSLQTASGYFPEGANSGGAMGTSMNPTFIPSAEHTPKLIATNGQSSFDF   600
 601  ASGSTNPFFPNRGDDELEFGLHNYGADGKSVHSETGWRPTSRSIVDDPHE   650
 651  YHEISDDEIAADKLDFGPSLLDEINSMFGSISAATGSHPKSPGFDHVNNK   700
 701  NEITEMSAKLGQKSGDTNGNKHGHGLLPTLSKKKSSGTVKPISVKDEKIL   750
 751  NHAIEIANEISARSMIDLVSDQTPVIHSPKRKFSFRFPHLSNNGSGDKSG   800
 801  GLGTSGSAHTPTHGNASPFPKKKNFTEELQSIPDIQSLIGKEGLEAYNSL   850
 851  IERKALLDIGPSPAATLLRHLDTDEFDLQSLHQSQRPMTLPTRGATQRVR   900
 901  KAELAAGLSRHNDENSNSLEACESPSYMTHGSYKFPEAQPTEQLPEPESP   950
 951  NPIPLPPREGKKQVKTSTKRHVRKYPLIIPANGLQRTLSKLADFGDEAAK  1000
1001  SPEISTSSQPQPGRAIEVVAAVRPSGMRRPSRPSEREYENMPTVGKESAH  1050
1051  TYQNLDKLTPADAAGLTDTASLQFESIMEADTSKEGILQSPDVTDGFYNF  1100
1101  SIQKEHYNKGKDAEFEATQISGLYVNDDELRNLDIESSRRTATPCSSCSA  1150
1151  LESEHSQPDALPSTESVSEVSRFSSVDNELAGNALFKKVRASVNMAMNRK  1200
1201  SVAETSLTSNQPGGASAKPQTEAEYFAATAARLADSNSVSCEDLLEFSDK  1250
1251  KPKGCERGVDSDEVRIMVKVLGKDSTPNRCLGALEFINWDVHKSIKLIKL  1300
1301  QNLVSEANLSLEASFEALQQHEWDLHTTAHKLNGLKL               1337

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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