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

NucPred

Fetching P06882 from www.uniprot.org...

The NucPred score for your sequence is 0.66 (see score help below)

   1  MMTLVLWVSTLLSSVCLVAANIFEYQVDAQPLRPCELQREKAFLKQDEYV    50
  51  PQCSEDGSFQTVQCQNDGQSCWCVDSDGTEVPGSRQLGRPTACLSFCQLH   100
 101  KQRILLSSYINSTDALYLPQCQDSGNYAPVQCDLQQVQCWCVDTEGMEVY   150
 151  GTRQQGRPTRCPRSCEIRSRRLLHGVGDKSPPQCDADGEFMPVQCKFVNT   200
 201  TDMMIFDLIHNYNRFPDAFVTFSAFRNRFPEVSGYCYCADSQGRELAETG   250
 251  LELLLDEIYDTIFAGLDQASTFTQSTMYRILQRRFLAIQLVISGRFRCPT   300
 301  KCEVEQFTATSFGHPYIPSCHRDGHYQTVQCQMERMCWCVDAQGIEIPGT   350
 351  RQQGQPLFCAKDQSCASERQQALSRLYFETPGYFSPQDLLSSEDRLVPVS   400
 401  GARLDISCPPRIKELFVDSGLLRSIAVERYQQLSESRSLLREAIRAIFPS   450
 451  RELAGLALQFTTNPKRLQQNLFGGTFLVNAAQLNLSGALGTRSTFNFSQF   500
 501  FQQFGLPGFLVRDRATDLAKLLPVSLDSSPTPVPLRVPEKRVAMNKSVVG   550
 551  TFGFKVNLQENQDALKFLVSLMELPEFLVFLQRAVSVPEDRARDLGDVME   600
 601  MVFSAQACKQTSGRFFVPSCTAEGSYEDIQCYAGECWCVNSQGKEVEGSR   650
 651  VSGGHPRCPTKCEKQRAQMQNLAGAQPAGSSFFVPTCTSEGYFLPVQCFN   700
 701  SECYCVDAEGQVIPGTQSTIGEPKLCPSVCQLQAEQAFLGVVGVLLSNSS   750
 751  MVPPISSVYIPQCSTSGQWMPVQCDGPHEQVFEWYERWNTQNSDGQELTT   800
 801  ATLLMKLMSYREVASTNFSLFLQSLYDAGQQSIFPVLAQYPSLQDVPQVV   850
 851  LEGATIQPGENIFLDPYIFWQILNGQLSQYPGPYSDFSMPLEHFNLRSCW   900
 901  CVDEAGQELDGTRTRAGEIPACPGPCEEVKFRVLKFIKETEEIVSASNAS   950
 951  SFPLGESFLVAKGIQLTSEELGLPPLYPSREAFSEKFLRGSEYAIRLAAQ  1000
1001  STLTFYQKLRASLGESNGTASLLWSGPYMPQCNTIGGWEPVQCHPGTGQC  1050
1051  WCVDGWGELIPGSLMARSSQMPQCPTSCELSRANGLISAWKQAGHQRNPG  1100
1101  PGDLFTPVCLQTGEYVRQQTSGTGAWCVDPSSGEGVPTNTNSSAQCPGLC  1150
1151  DALKSRVLSRKVGLGYTPVCEALDGGFSPVQCDLAQGSCWCVLASGEEVP  1200
1201  GTRVVGTQPACESPQCPLPFSGSDVTDGVVFCETASSSGVTTVQQCQLFC  1250
1251  RQGLRNVFSPGPLICNLESQRWVTLPLPRACQRPQLWQTMQTQAHFQLLL  1300
1301  PPGKMCSIDYSGLLQAFQVFILDELITRGFCQIQVKTFGTLVSRTVCDNS  1350
1351  SIQVGCLTAERLGVNATWKLQLEDISVGSLPNLHSIERALMGQDLLGRFA  1400
1401  NLIQSGKFQLHLDSKTFSADTILYFLNGDRFVTSPMTQLGCLEGFYRVST  1450
1451  TSQDPLGCVKCPEGSFSQDGKCTPCPAGTYQGQAGSSACIPCPRGRTTTI  1500
1501  TGAFSKTHCVTDCQRDEAGLQCDQNGQYQANQKDMDSGEVFCVDSEGQRL  1550
1551  QWLQTEAGLSESQCLMMRKFEKAPESKVIFDASSPVIVKSRVPSANSPLV  1600
1601  QCLADCADDEACSFVTVSSMSSEVSCDLYSWTRDNFACVTSDQEEDAVDS  1650
1651  LKETSFGSLRCQVKVRNSGKDSLAVYVKKGHEFTASGQKSFEPTGFQNVL  1700
1701  SGLYSSVVFSALGTNLTDTHLFCLLACDQDSCCDGFIVTQVKEGPTICGL  1750
1751  LSAPDILVCHINDWRDASDTQANGTCAGVTYDQGSRQMTMSLGGQEFLQG  1800
1801  LTLLEGTQDSFISFQQVYLWKDSDIGSRPESMGCGRGMVPKSEAPEGADM  1850
1851  ATELFSPVDITQVIVNTSHSLPSQQYWLSTHLFSAEQANLWCLSRCAQEP  1900
1901  VFCQLADIMESSSLYFTCSLYPEAQVCDNDVESNAKNCSQILPRQPTALF  1950
1951  QRKVVLNDRVKNFYTRLPFQKLSGISIRDRIPMSEKLISNGFFECERLCD  2000
2001  RDPCCTGFGFLNVSQMQGGEMTCLTLNSMGIQTCSEENGATWRILDCGSE  2050
2051  DTEVHTYPFGWYQKPAVWSDAPSFCPSAALQSLTEEKVALDSWQTLALSS  2100
2101  VIIDPSIKHFDVAHISISATRNFSLAQDFCLQECSRHQDCLVTTLQIQQG  2150
2151  VVRCVFYPDIQSCEHSLRSKTCWLLLHEEAAYIYRKSGAPLHQSDGISTP  2200
2201  SVHIDSFGQLQGGSQVVKVGTAWKQVYQFLGVPYAAPPLAENRFQAPEVL  2250
2251  NWTGSWDATKLRSSCWQPGTRTPTPPQISEDCLYLNVFVPENLVSNASVL  2300
2301  VFFHNTVEMEGSGGQLNIDGSILAAVGNLIVVTANYRLGVFGFLSSGSDE  2350
2351  VAGNWGLLDQVAALTWVQTHIGAFGGDPQRVTLAADRGGADVASIHLLIT  2400
2401  RPTRLQLFRKALLMGGSALSPAAIISPDRAQQQAAALAKEVGCPNSSVQE  2450
2451  VVSCFRQKPANILNEAQTKLLAVSGPFHYWGPVVDGQYLRELPSRRLKRP  2500
2501  LPVKVDLLIGGSQDDGLINRAKAVKQFEESQGRTNSKTAFYQALQNSLGG  2550
2551  EDSDARILAAAIWYYSLEHSTDDYASFSRALENATRDYFIICPIVNMASL  2600
2601  WARRTRGNVFMYHVPESYGHGSLELLADVQYAFGLPFYSAYQGYFSTEEQ  2650
2651  SLSLKVMQYFSNFIRSGNPNYPHEFSQKAAEFATPWPDFVPGAGGESYKE  2700
2701  LSAQLPNRQGLKKADCSFWSKYIQTLKDADGAKDAQLTKSGEEDLEVGPG  2750
2751  SEEDFSGSLEPVPKSYSK                                  2768

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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