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

NucPred

Fetching Q96RK0 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MKPMKKACTGLSGPGSGSKSPPATRAKALRRRGAGEGDKPEEEDDEAQQP    50
  51  QPQSGPEEAEEGEEEEAERGPGAEGPPLELHPGDPAPGPAEDPKGDGEAG   100
 101  RWEPSLSRKTATFKSRAPKKKYVEEHGAGSSGVAGAPEERVRTPEEASGL   150
 151  GVPPRPPTSTRSSSTDTASEHSADLEDEPAEACGPGPWPPGSTSGSYDLR   200
 201  QLRSQRVLARRGDGLFLPAVVRQVRRSQDLGVQFPGDRALTFYEGVPGAG   250
 251  VDVVLDATPPPGALVVGTAVCTCVEPGVAAYREGVVVEVATKPAAYKVRL   300
 301  SPGPSSQPGLPGSLPQPPQPLHREPEEAVWVARSSLRLLRPPWEPETMLR   350
 351  KPPTGPEEEQAEPGATLPPCPAALDPKQPEDAEVSKISFGGNLGTHCEEG   400
 401  EEKHPPALGTPALLPLPPPQLLSPPPKSPAFVGPGRPGEQPSPCQEGSQG   450
 451  GSRSSSVASLEKGTAPAARARTPLTAAQQKYKKGDVVCTPSGIRKKFNGK   500
 501  QWRRLCSRDGCMKESQRRGYCSRHLSMRTKEMEGLADSGPGGAGRPAAVA   550
 551  AREGSTEFDWGDETSRDSEASSVAARGDSRPRLVAPADLSRFEFDECEAA   600
 601  VMLVSLGSSRSGTPSFSPVSTQSPFSPAPSPSPSPLFGFRPANFSPINAS   650
 651  PVIQRTAVRSRHLSASTPKAGVLTPPDLGPHPPPPAPRERHSSGILPTFQ   700
 701  TNLTFTVPISPGRRKTELLPHPGALGAPGAGGGGAAPDFPKSDSLDSGVD   750
 751  SVSHTPTPSTPAGFRAVSPAVPFSRSRQPSPLLLLPPPAGLTSDPGPSVR   800
 801  RVPAVQRDSPVIVRNPDVPLPSKFPGEVGTAGEVRAGGPGRGCRETPVPP   850
 851  GVASGKPGLPPPLPAPVPITVPPAAPTAVAQPMPAFGLASSPFQPVAFHP   900
 901  SPAALLPVLVPSSYTSHPAPKKEVIMGRPGTVWTNVEPRSVAVFPWHSLV   950
 951  PFLAPSQPDPSVQPSEAQQPASHPVASNQSKEPAESAAVAHERPPGGTGS  1000
1001  ADPERPPGATCPESPGPGPPHPLGVVESGKGPPPTTEEEASGPPGEPRLD  1050
1051  SETESDHDDAFLSIMSPEIQLPLPPGKRRTQSLSALPKERDSSSEKDGRS  1100
1101  PNKREKDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYAL  1150
1151  GPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKKSSSEAKPTSLGLAGG  1200
1201  HKETRERSMSETGTAAAPGVSSELLSVAAQTLLSSDTKAPGSSSCGAERL  1250
1251  HTVGGPGSARPRAFSHSGVHSLDGGEVDSQALQELTQMVSGPASYSGPKP  1300
1301  STQYGAPGPFAAPGEGGALAATGRPPLLPTRASRSQRAASEDMTSDEERM  1350
1351  VICEEEGDDDVIADDGFGTTDIDLKCKERVTDSESGDSSGEDPEGNKGFG  1400
1401  RKVFSPVIRSSFTHCRPPLDPEPPGPPDPPVAFGKGYGSAPSSSASSPAS  1450
1451  SSASAATSFSLGSGTFKAQESGQGSTAGPLRPPPPGAGGPATPSKATRFL  1500
1501  PMDPATFRRKRPESVGGLEPPGPSVIAAPPSGGGNILQTLVLPPNKEEQE  1550
1551  GGGARVPSAPAPSLAYGAPAAPLSRPAATMVTNVVRPVSSTPVPIASKPF  1600
1601  PTSGRAEASPNDTAGARTEMGTGSRVPGGSPLGVSLVYSDKKSAAATSPA  1650
1651  PHLVAGPLLGTVGKAPATVTNLLVGTPGYGAPAPPAVQFIAQGAPGGGTT  1700
1701  AGSGAGAGSGPNGPVPLGILQPGALGKAGGITQVQYILPTLPQQLQVAPA  1750
1751  PAPAPGTKAAAPSGPAPTTSIRFTLPPGTSTNGKVLAATAPTPGIPILQS  1800
1801  VPSAPPPKAQSVSPVQAPPPGGSAQLLPGKVLVPLAAPSMSVRGGGAGQP  1850
1851  LPLVSPPFSVPVQNGAQPPSKIIQLTPVPVSTPSGLVPPLSPATLPGPTS  1900
1901  QPQKVLLPSSTRITYVQSAGGHALPLGTSPASSQAGTVTSYGPTSSVALG  1950
1951  FTSLGPSGPAFVQPLLSAGQAPLLAPGQVGVSPVPSPQLPPACAAPGGPV  2000
2001  ITAFYSGSPAPTSSAPLAQPSQAPPSLVYTVATSTTPPAATILPKGPPAP  2050
2051  ATATPAPTSPFPSATAGSMTYSLVAPKAQRPSPKAPQKVKAAIASIPVGS  2100
2101  FEAGASGRPGPAPRQPLEPGPVREPTAPESELEGQPTPPAPPPLPETWTP  2150
2151  TARSSPPLPPPAEERTSAKGPETMASKFPSSSSDWRVPGQGLENRGEPPT  2200
2201  PPSPAPAPAVAPGGSSESSSGRAAGDTPERKEAAGTGKKVKVRPPPLKKT  2250
2251  FDSVDNRVLSEVDFEERFAELPEFRPEEVLPSPTLQSLATSPRAILGSYR  2300
2301  KKRKNSTDLDSAPEDPTSPKRKMRRRSSCSSEPNTPKSAKCEGDIFTFDR  2350
2351  TGTEAEDVLGELEYDKVPYSSLRRTLDQRRALVMQLFQDHGFFPSAQATA  2400
2401  AFQARYADIFPSKVCLQLKIREVRQKIMQAATPTEQPPGAEAPLPVPPPT  2450
2451  GTAAAPAPTPSPAGGPDPTSPSSDSGTAQAAPPLPPPPESGPGQPGWEGA  2500
2501  PQPSPPPPGPSTAATGR                                   2517

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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