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

NucPred

Fetching P46821 from www.uniprot.org...

The NucPred score for your sequence is 0.70 (see score help below)

   1  MATVVVEATEPEPSGSIANPAASTSPSLSHRFLDSKFYLLVVVGEIVTEE    50
  51  HLRRAIGNIELGIRSWDTNLIECNLDQELKLFVSRHSARFSPEVPGQKIL   100
 101  HHRSDVLETVVLINPSDEAVSTEVRLMITDAARHKLLVLTGQCFENTGEL   150
 151  ILQSGSFSFQNFIEIFTDQEIGELLSTTHPANKASLTLFCPEEGDWKNSN   200
 201  LDRHNLQDFINIKLNSASILPEMEGLSEFTEYLSESVEVPSPFDILEPPT   250
 251  SGGFLKLSKPCCYIFPGGRGDSALFAVNGFNMLINGGSERKSCFWKLIRH   300
 301  LDRVDSILLTHIGDDNLPGINSMLQRKIAELEEEQSQGSTTNSDWMKNLI   350
 351  SPDLGVVFLNVPENLKNPEPNIKMKRSIEEACFTLQYLNKLSMKPEPLFR   400
 401  SVGNTIDPVILFQKMGVGKLEMYVLNPVKSSKEMQYFMQQWTGTNKDKAE   450
 451  FILPNGQEVDLPISYLTSVSSLIVWHPANPAEKIIRVLFPGNSTQYNILE   500
 501  GLEKLKHLDFLKQPLATQKDLTGQVPTPVVKQTKLKQRADSRESLKPAAK   550
 551  PLPSKSVRKESKEETPEVTKVNHVEKPPKVESKEKVMVKKDKPIKTETKP   600
 601  SVTEKEVPSKEEPSPVKAEVAEKQATDVKPKAAKEKTVKKETKVKPEDKK   650
 651  EEKEKPKKEVAKKEDKTPIKKEEKPKKEEVKKEVKKEIKKEEKKEPKKEV   700
 701  KKETPPKEVKKEVKKEEKKEVKKEEKEPKKEIKKLPKDAKKSSTPLSEAK   750
 751  KPAALKPKVPKKEESVKKDSVAAGKPKEKGKIKVIKKEGKAAEAVAAAVG   800
 801  TGATTAAVMAAAGIAAIGPAKELEAERSLMSSPEDLTKDFEELKAEEVDV   850
 851  TKDIKPQLELIEDEEKLKETEPVEAYVIQKEREVTKGPAESPDEGITTTE   900
 901  GEGECEQTPEELEPVEKQGVDDIEKFEDEGAGFEESSETGDYEEKAETEE   950
 951  AEEPEEDGEEHVCVSASKHSPTEDEESAKAEADAYIREKRESVASGDDRA  1000
1001  EEDMDEAIEKGEAEQSEEEADEEDKAEDAREEEYEPEKMEAEDYVMAVVD  1050
1051  KAAEAGGAEEQYGFLTTPTKQLGAQSPGREPASSIHDETLPGGSESEATA  1100
1101  SDEENREDQPEEFTATSGYTQSTIEISSEPTPMDEMSTPRDVMSDETNNE  1150
1151  ETESPSQEFVNITKYESSLYSQEYSKPADVTPLNGFSEGSKTDATDGKDY  1200
1201  NASASTISPPSSMEEDKFSRSALRDAYCSEVKASTTLDIKDSISAVSSEK  1250
1251  VSPSKSPSLSPSPPSPLEKTPLGERSVNFSLTPNEIKVSAEAEVAPVSPE  1300
1301  VTQEVVEEHCASPEDKTLEVVSPSQSVTGSAGHTPYYQSPTDEKSSHLPT  1350
1351  EVIEKPPAVPVSFEFSDAKDENERASVSPMDEPVPDSESPIEKVLSPLRS  1400
1401  PPLIGSESAYESFLSADDKASGRGAESPFEEKSGKQGSPDQVSPVSEMTS  1450
1451  TSLYQDKQEGKSTDFAPIKEDFGQEKKTDDVEAMSSQPALALDERKLGDV  1500
1501  SPTQIDVSQFGSFKEDTKMSISEGTVSDKSATPVDEGVAEDTYSHMEGVA  1550
1551  SVSTASVATSSFPEPTTDDVSPSLHAEVGSPHSTEVDDSLSVSVVQTPTT  1600
1601  FQETEMSPSKEECPRPMSISPPDFSPKTAKSRTPVQDHRSEQSSMSIEFG  1650
1651  QESPEQSLAMDFSRQSPDHPTVGAGVLHITENGPTEVDYSPSDMQDSSLS  1700
1701  HKIPPMEEPSYTQDNDLSELISVSQVEASPSTSSAHTPSQIASPLQEDTL  1750
1751  SDVAPPRDMSLYASLTSEKVQSLEGEKLSPKSDISPLTPRESSPLYSPTF  1800
1801  SDSTSAVKEKTATCHSSSSPPIDAASAEPYGFRASVLFDTMQHHLALNRD  1850
1851  LSTPGLEKDSGGKTPGDFSYAYQKPEETTRSPDEEDYDYESYEKTTRTSD  1900
1901  VGGYYYEKIERTTKSPSDSGYSYETIGKTTKTPEDGDYSYEIIEKTTRTP  1950
1951  EEGGYSYDISEKTTSPPEVSGYSYEKTERSRRLLDDISNGYDDSEDGGHT  2000
2001  LGDPSYSYETTEKITSFPESEGYSYETSTKTTRTPDTSTYCYETAEKITR  2050
2051  TPQASTYSYETSDLCYTAEKKSPSEARQDVDLCLVSSCEYKHPKTELSPS  2100
2101  FINPNPLEWFASEEPTEESEKPLTQSGGAPPPPGGKQQGRQCDETPPTSV  2150
2151  SESAPSQTDSDVPPETEECPSITADANIDSEDESETIPTDKTVTYKHMDP  2200
2201  PPAPVQDRSPSPRHPDVSMVDPEALAIEQNLGKALKKDLKEKTKTKKPGT  2250
2251  KTKSSSPVKKSDGKSKPLAASPKPAGLKESSDKVSRVASPKKKESVEKAA  2300
2301  KPTTTPEVKAARGEEKDKETKNAANASASKSAKTATAGPGTTKTTKSSAV  2350
2351  PPGLPVYLDLCYIPNHSNSKNVDVEFFKRVRSSYYVVSGNDPAAEEPSRA  2400
2401  VLDALLEGKAQWGSNMQVTLIPTHDSEVMREWYQETHEKQQDLNIMVLAS  2450
2451  SSTVVMQDESFPACKIEL                                  2468

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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