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

NucPred

Fetching Q9Y2I7 from www.uniprot.org...

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

   1  MATDDKTSPTLDSANDLPRSPTSPSHLTHFKPLTPDQDEPPFKSAYSSFV    50
  51  NLFRFNKERAEGGQGEQQPLSGSWTSPQLPSRTQSVRSPTPYKKQLNEEL   100
 101  QRRSSALDTRRKAEPTFGGHDPRTAVQLRSLSTVLKRLKEIMEGKSQDSD   150
 151  LKQYWMPDSQCKECYDCSEKFTTFRRRHHCRLCGQIFCSRCCNQEIPGKF   200
 201  MGYTGDLRACTYCRKIALSYAHSTDSNSIGEDLNALSDSACSVSVLDPSE   250
 251  PRTPVGSRKASRNIFLEDDLAWQSLIHPDSSNTPLSTRLVSVQEDAGKSP   300
 301  ARNRSASITNLSLDRSGSPMVPSYETSVSPQANRTYVRTETTEDERKILL   350
 351  DSVQLKDLWKKICHHSSGMEFQDHRYWLRTHPNCIVGKELVNWLIRNGHI   400
 401  ATRAQAIAIGQAMVDGRWLDCVSHHDQLFRDEYALYRPLQSTEFSETPSP   450
 451  DSDSVNSVEGHSEPSWFKDIKFDDSDTEQIAEEGDDNLANSASPSKRTSV   500
 501  SSFQSTVDSDSAASISLNVELDNVNFHIKKPSKYPHVPPHPADQKEYLIS   550
 551  DTGGQQLSISDAFIKESLFNRRVEEKSKELPFTPLGWHHNNLELLREENG   600
 601  EKQAMERLLSANHNHMMALLQQLLHSDSLSSSWRDIIVSLVCQVVQTVRP   650
 651  DVKNQDDDMDIRQFVHIKKIPGGKKFDSVVVNGFVCTKNIAHKKMSSCIK   700
 701  NPKILLLKCSIEYLYREETKFTCIDPIVLQEREFLKNYVQRIVDVRPTLV   750
 751  LVEKTVSRIAQDMLLEHGITLVINVKSQVLERISRMTQGDLVMSMDQLLT   800
 801  KPHLGTCHKFYMQIFQLPNEQTKTLMFFEGCPQHLGCTIKLRGGSDYELA   850
 851  RVKEILIFMICVAYHSQLEISFLMDEFAMPPTLMQNPSFHSLIEGRGHEG   900
 901  AVQEQYGGGSIPWDPDIPPESLPCDDSSLLELRIVFEKGEQENKNLPQAV   950
 951  ASVKHQEHSTTACPAGLPCAFFAPVPESLLPLPVDDQQDALGSEQPETLQ  1000
1001  QTVVLQDPKSQIRAFRDPLQDDTGLYVTEEVTSSEDKRKTYSLAFKQELK  1050
1051  DVILCISPVITFREPFLLTEKGMRCSTRDYFAEQVYWSPLLNKEFKEMEN  1100
1101  RRKKQLLRDLSGLQGMNGSIQAKSIQVLPSHELVSTRIAEHLGDSQSLGR  1150
1151  MLADYRARGGRIQPKNSDPFAHSKDASSTSSGQSGSKNEGDEERGLILSD  1200
1201  AVWSTKVDCLNPINHQRLCVLFSSSSAQSSNAPSACVSPWIVTMEFYGKN  1250
1251  DLTLGIFLERYCFRPSYQCPSMFCDTPMVHHIRRFVHGQGCVQIILKELD  1300
1301  SPVPGYQHTILTYSWCRICKQVTPVVALSNESWSMSFAKYLELRFYGHQY  1350
1351  TRRANAEPCGHSIHHDYHQYFSYNQMVASFSYSPIRLLEVCVPLPKIFIK  1400
1401  RQAPLKVSLLQDLKDFFQKVSQVYVAIDERLASLKTDTFSKTREEKMEDI  1450
1451  FAQKEMEEGEFKNWIEKMQARLMSSSVDTPQQLQSVFESLIAKKQSLCEV  1500
1501  LQAWNNRLQDLFQQEKGRKRPSVPPSPGRLRQGEESKISAMDASPRNISP  1550
1551  GLQNGEKEDRFLTTLSSQSSTSSTHLQLPTPPEVMSEQSVGGPPELDTAS  1600
1601  SSEDVFDGHLLGSTDSQVKEKSTMKAIFANLLPGNSYNPIPFPFDPDKHY  1650
1651  LMYEHERVPIAVCEKEPSSIIAFALSCKEYRNALEELSKATQWNSAEEGL  1700
1701  PTNSTSDSRPKSSSPIRLPEMSGGQTNRTTETEPQPTKKASGMLSFFRGT  1750
1751  AGKSPDLSSQKRETLRGADSAYYQVGQTGKEGTENQGVEPQDEVDGGDTQ  1800
1801  KKQLINPHVELQFSDANAKFYCRLYYAGEFHKMREVILDSSEEDFIRSLS  1850
1851  HSSPWQARGGKSGAAFYATEDDRFILKQMPRLEVQSFLDFAPHYFNYITN  1900
1901  AVQQKRPTALAKILGVYRIGYKNSQNNTEKKLDLLVMENLFYGRKMAQVF  1950
1951  DLKGSLRNRNVKTDTGKESCDVVLLDENLLKMVRDNPLYIRSHSKAVLRT  2000
2001  SIHSDSHFLSSHLIIDYSLLVGRDDTSNELVVGIIDYIRTFTWDKKLEMV  2050
2051  VKSTGILGGQGKMPTVVSPELYRTRFCEAMDKYFLMVPDHWTGLGLNC    2098

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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