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

NucPred

Fetching P38111 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MESHVKYLDELILAIKDLNSGVDSKVQIKKVPTDPSSSQEYAKSLKILNT    50
  51  LIRNLKDQRRNNIMKNDTIFSKTVSALALLLEYNPFLLVMKDSNGNFEIQ   100
 101  RLIDDFLNISVLNYDNYHRIWFMRRKLGSWCKACVEFYGKPAKFQLTAHF   150
 151  ENTMNLYEQALTEVLLGKTELLKFYDTLKGLYILLYWFTSEYSTFGNSIA   200
 201  FLDSSLGFTKFDFNFQRLIRIVLYVFDSCELAALEYAEIQLKYISLVVDY   250
 251  VCNRTISTALDAPALVCCEQLKFVLTTMHHFLDNKYGLLDNDPTMAKGIL   300
 301  RLYSLCISNDFSKCFVDHFPIDQWADFSQSEHFPFTQLTNKALSIVYFDL   350
 351  KRRSLPVEALKYDNKFNIWVYQSEPDSSLKNVTSPFDDRYKQLEKLRLLV   400
 401  LKKFNKTERGTLLKYRVNQLSPGFFQRAGNDFKLILNEASVSIQTCFKTN   450
 451  NITRLTSWTVILGRLACLESEKFSGTLPNSTKDMDNWYVCHLCDIEKTGN   500
 501  PFVRINPNRPEAAGKSEIFRILHSNFLSHPNIDEFSESLLSGILFSLHRI   550
 551  FSHFQPPKLTDGNGQINKSFKLVQKCFMNSNRYLRLLSTRIIPLFNISDS   600
 601  HNSEDEHTATLIKFLQSQKLPVVKENLVIAWTQLTLTTSNDVFDTLLLKL   650
 651  IDIFNSDDYSLRIMMTLQIKNMAKILKKTPYQLLSPILPVLLRQLGKNLV   700
 701  ERKVGFQNLIELLGYSSKTILDIFQRYIIPYAIIQYKSDVLSEIAKIMCD   750
 751  GDTSLINQMKVNLLKKNSRQIFAVALVKHGLFSLDILETLFLNRAPTFDK   800
 801  GYITAYLPDYKTLAEITKLYKNSVTKDASDSENANMILCSLRFLITNFEK   850
 851  DKRHGSKYKNINNWTDDQEQAFQKKLQDNILGIFQVFSSDIHDVEGRTTY   900
 901  YEKLRVINGISFLIIYAPKKSIISALAQISICLQTGLGLKEVRYEAFRCW   950
 951  HLLVRHLNDEELSTVIDSLIAFILQKWSEFNGKLRNIVYSILDTLIKEKS  1000
1001  DLILKLKPYTTLALVGKPELGILARDGQFARMVNKIRSTTDLIPIFANNL  1050
1051  KSSNKYVINQNLDDIEVYLRRKQTERSIDFTPKKVGQTSDITLVLGALLD  1100
1101  TSHKFRNLDKDLCEKCAKCISMIGVLDVTKHEFKRTTYSENEVYDLNDSV  1150
1151  QTIKFLIWVINDILVPAFWQSENPSKQLFVALVIQESLKYCGLSSESWDM  1200
1201  NHKELYPNEAKLWEKFNSVSKTTIYPLLSSLYLAQSWKEYVPLKYPSNNF  1250
1251  KEGYKIWVKRFTLDLLKTGTTENHPLHVFSSLIREDDGSLSNFLLPYISL  1300
1301  DIIIKAEKGTPYADILNGIIIEFDSIFTCNLEGMNNLQVDSLRMCYESIF  1350
1351  RVFEYCKKWATEFKQNYSKLHGTFIIKDTKTTNMLLRIDEFLRTTPSDLL  1400
1401  AQRSLETDSFERSALYLEQCYRQNPHDKNQNGQLLKNLQITYEEIGDIDS  1450
1451  LDGVLRTFATGNLVSKIEELQYSENWKLAQDCFNVLGKFSDDPKTTTRML  1500
1501  KSMYDHQLYSQIISNSSFHSSDGKISLSPDVKEWYSIGLEAANLEGNVQT  1550
1551  LKNWVEQIESLRNIDDREVLLQYNIAKALIAISNEDPLRTQKYIHNSFRL  1600
1601  IGTNFITSSKETTLLKKQNLLMKLHSLYDLSFLSSAKDKFEYKSNTTILD  1650
1651  YRMERIGADFVPNHYILSMRKSFDQLKMNEQADADLGKTFFTLAQLARNN  1700
1701  ARLDIASESLMHCLERRLPQAELEFAEILWKQGENDRALKIVQEIHEKYQ  1750
1751  ENSSVNARDRAAVLLKFTEWLDLSNNSASEQIIKQYQDIFQIDSKWDKPY  1800
1801  YSIGLYYSRLLERKKAEGYITNGRFEYRAISYFLLAFEKNTAKVRENLPK  1850
1851  VITFWLDIAAASISEAPGNRKEMLSKATEDICSHVEEALQHCPTYIWYFV  1900
1901  LTQLLSRLLHSHQSSAQIIMHILLSLAVEYPSHILWYITALVNSNSSKRV  1950
1951  LRGKHILEKYRQHSQNPHDLVSSALDLTKALTRVCLQDVKSITSRSGKSL  2000
2001  EKDFKFDMNVAPSAMVVPVRKNLDIISPLESNSMRGYQPFRPVVSIIRFG  2050
2051  SSYKVFSSLKKPKQLNIIGSDGNIYGIMCKKEDVRQDNQYMQFATTMDFL  2100
2101  LSKDIASRKRSLGINIYSVLSLREDCGILEMVPNVVTLRSILSTKYESLK  2150
2151  IKYSLKSLHDRWQHTAVDGKLEFYMEQVDKFPPILYQWFLENFPDPINWF  2200
2201  NARNTYARSYAVMAMVGHILGLGDRHCENILLDIQTGKVLHVDFDCLFEK  2250
2251  GKRLPVPEIVPFRLTPNLLDALGIIGTEGTFKKSSEVTLALMRKNEVALM  2300
2301  NVIETIMYDRNMDHSIQKALKVLRNKIRGIDPQDGLVLSVAGQTETLIQE  2350
2351  ATSEDNLSKMYIGWLPFW                                  2368

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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