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

NucPred

Fetching Q80TP3 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MTSIHFVVHPLPGTEDQLNDRLREVSEKLNKYNLNSHPPLNVLEQATIKQ    50
  51  CVVGPNHAAFLLEDGRICRIGFSVQPDRLELGKPDNNDGSKLNSSSGTGR   100
 101  TSRPGRTSDSPWFLSGSETLGRLAGNTLGSRWSSGVGGSGGGSSGRSSAG   150
 151  ARDSRRQTRVIRTGRDRGSGLLGSQPQPVIPASVIPEELISQAQVVLQGK   200
 201  SRSVIIRELQRTNLDVNLAVNNLLSRDDEDGDDGDDTASESYLPGEDLMS   250
 251  LLDADIHSAHPSVIIDADAMFSEDISYFGYPSFRRSSLSRLGSSRERDSE   300
 301  LLRERESVLRLRERRWLDGASFDNERGSTSKEGESNPDKKNTPVQSPVSL   350
 351  GEDLQWWPDKDGTKFTCIGALYSELLAVSSKGELYQWKWSESEPYRNAQN   400
 401  PSLHHPRATFLGLTNEKIVLLSANSIRATVATENNKVATWVDETLSSVAS   450
 451  KLEHTAQTYSELQGERIVSLHCCALYTCAQLENNLYWWGVVPFSQRKKML   500
 501  EKARAKNKKPKSSAGISSMPNITVGTQVCLRNNPLYHAGAVAFSISAGIP   550
 551  KVGVLMESVWNMNDSCRFQLRSPESLKSMEKASKTLETKPESKQEPVKTE   600
 601  MGPPPSPASTCSDASSIASSASMPYKRRRSTPAPREEEKVNEEQWPLREV   650
 651  VFVEDVKNVPVGKVLKVDGAYVAVKFPGTSTNTTCQNSSGPDADPSSLLQ   700
 701  DCRLLRIDELQVVKTGGTPKVPDCFQRTPKKLCIPEKTEILAVNVDSKGV   750
 751  HAVLKTGSWVRYCVFDLATGKAEQENNFPTSSVAFLGQDERSVAIFTAGQ   800
 801  ESPIVLRDGNGTIYPMAKDCMGGIRDPDWLDLPPISSLGMGVHSLINLPA   850
 851  NSTIKKKAAIIIMAVEKQTLMQHILRCDYEACRQYLVNLEQAVVLEQNRQ   900
 901  MLQTFISHRCDGNRNILHACVSVCFPTSNKETKEEEEAERSERNTFAERL   950
 951  SAVEAIANAISVVSSNGPGNRAGSSNSRSLRLREMMRRSLRAAGLGRHEA  1000
1001  GASSSDHQDPVSPPIAPPSWVPDPPSMDPDGDIDFILAPAVGSLTTAATG  1050
1051  SGQGPSTSTIPGPSTEPSVVESKDRKANAHFILKLLCDSAVLQPYLRELL  1100
1101  SAKDARGMTPFMSAVSGRAYSAAITILETAQKIAKAEVSASEKEEDVFMG  1150
1151  MVCPSGTNPDDSPLYVLCCNDTCSFTWTGAEHINQDIFECRTCGLLESLC  1200
1201  CCTECARVCHKGHDCKLKRTSPTAYCDCWEKCKCKTLIAGQKSARLDLLY  1250
1251  RLLTATNLVTLPNSRGEHLLLFLVQTVARQTVEHCQYRPPRIREDRNRKT  1300
1301  ASPEDSDMPDHDLEPPRFAQLALERVLQDWNALRSMIMFGSQENKDPLSA  1350
1351  SSRIGHLLPEEQVYLNQQSGTIRLDCFTHCLIVKCTADILLLDTLLGTLV  1400
1401  KELQNKYTPGRREEAIAVTMRFLRSVARVFVILSVEMASSKKKNNFIPQP  1450
1451  IGKCKRVFQALLPYAVEELCNVAESLIVPVRMGIARPTAPFTLASTSIDA  1500
1501  MQGSEELFSVEPLPPRPSSDQASSSSQSQSSYIIRNPQQRRISQSQPVRG  1550
1551  RDEEQDDIVSADVEEVEVVEGVAGEEDHHDEQEEHGEENAEAEGHHDEHD  1600
1601  EDGSDMELDLLAAAETESDSESNHSNQDNASGRRSVVTAATAGSEAGASS  1650
1651  VPAFFSEDDSQSNDSSDSDSSSSQSDDIEQETFMLDEPLERTTNSSHANG  1700
1701  AAQAPRSMQWAVRNPQHQRAASTAPSSTSTPAASSAGLIYIDPSNLRRSG  1750
1751  TISTSAAAAAAALEASNASSYLTSASSLARAYSIVIRQISDLMGLIPKYN  1800
1801  HLVYSQIPAAVKLTYQDAVNLQNYVEEKLIPTWNWMVSVMDSTEAQLRYG  1850
1851  SALASAGDPGHPNHPLHASQNSARRERMTAREEASLRTLEGRRRATLLSA  1900
1901  RQGMMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLKHVAYVFQALIY  1950
1951  WIKAMNQQTTLDTPQLERKRTRELLELGIDNEDSEHENDDDTSQSATLND  2000
2001  KDDDSLPAETGQNHPFFRRSDSMTFLGCIPPNPFEVPLAEAIPLADQPHL  2050
2051  LQPNARKEDLFGRPSQGLYSSSAGSGKCIVEVTMDRNCLEVLPTKMSYAA  2100
2101  NLKNVMNMQNRQKKEGEEQSLLAEEADSSKPGPSAPDVAAQLKSSLLAEI  2150
2151  GLTESEGPPLTSFRPQCSFMGMVISHDMLLGRWRLSLELFGRVFMEDVGA  2200
2201  EPGSILTELGGFEVKESKFRREMEKLRNQQSRDLSLEVDRDRDLLIQQTM  2250
2251  RQLNNHFGRRCATTPMAVHRVKVTFKDEPGEGSGVARSFYTAIAQAFLSN  2300
2301  EKLPNLDCIQNANKGTHTSLMQRLRNRGERDREREREREMRRSSGLRAGS  2350
2351  RRDRDRDFRRQLSIDTRPFRPASEGNPSDDPDPLPAHRQALGERLYPRVQ  2400
2401  AMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAHGREN  2450
2451  GADSILDLGLLDSSEKVQENRKRHGSSRSVVDMDLEDTDDGDDNAPLFYQ  2500
2501  PGKRGFYTPRPGKNTEARLNCFRNIGRILGLCLLQNELCPITLNRHVIKV  2550
2551  LLGRKVNWHDFAFFDPVMYESLRQLILASQSSDADAVFSAMDLAFAIDLC  2600
2601  KEEGGGQVELIPNGVNIPVTPQNVYEYVRKYAEHRMLVVAEQPLHAMRKG  2650
2651  LLDVLPKNSLEDLTAEDFRLLVNGCGEVNVQMLISFTSFNDESGENAEKL  2700
2701  LQFKRWFWSIVEKMSMTERQDLVYFWTSSPSLPASEEGFQPMPSITIRPP  2750
2751  DDQHLPTANTCISRLYVPLYSSKQILKQKLLLAIKTKNFGFV          2792

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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