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

NucPred

Fetching O74630 from www.uniprot.org...

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

   1  MTSLNDIVNKLSSSKIKTRSDALQNLRSYIIYSRNGNSLNQEDALIIEKA    50
  51  IKRAFELEWQISANHGKRQISKASQEQKLQDISYLLRTCVESYILLFREP   100
 101  HILALLDIILRHTFTANGSICEVVCLNFSKALRLLLSHSPHLHHLRFSDW   150
 151  QSLVSYCCQAIEKLSIAEETYVSDSEEEPISQKNYQEISIWKSHDVIRVK   200
 201  QEVVELIYVMRSLVQWYAAPINFVSEQLLKFFEFFFYAYTEETDAHLPAL   250
 251  QCLFQLCAYAIPNCNDYSASVVLLVFKILINSDKWKRLDLRLQLIQCLAI   300
 301  SYPLWSNSETWDPHRSIRSFNLDLLNSSFFSLKNFLNFFGKRSSLSLANF   350
 351  RFHTVEPKNNIAKLYDPRLHLFFSLRHNSFFESYFIYFFLAKLILLKKTV   400
 401  LSLASTEQANKKQKTCSQIEELLLQAELANISASSFSLQLMVIITAISDN   450
 451  LTNDDLLSIQKMSLNFTEKKNELQSWSFFILFNICYNKAYSSMLTTSCKK   500
 501  EILAAASRGLLNSVTSPVCYQILTYFNMYRPLCFASIFPFIKQQFILFND   550
 551  YSPMLSYEAIDYWKSLYILLNENLFVGQSSFKSVFLKWLKWHLYHLFSKE   600
 601  GELPFFSFTDSSIIIFDLLMMIFYRPLSLSYITTEIRSPFERNLFHLKEA   650
 651  WSPVTLRFPYTTDEICKQSTEGCYPFNSNHTIDCDSLQNVIKMLESSIDE   700
 701  ISSASYDKDELDKETPSFEAVMIFSQISFLCGFLNCFIQKKGIHNVTPNN   750
 751  LVIFKNLFPEVLSFVKSNHSYDPIINCISTNLQFTISDEPKHLRYEIGSD   800
 801  LIRSTHFRDSNPLKTLVLYIMDMASKNVFIKPQEFDHDEYFSQEEEDIYR   850
 851  PENLIRNHQILGLMEGSLEQIRNTDLFILQKYIDYFSSHPHDSLINILHL   900
 901  YPIETFCFGMSAIGAYFLDVARTSEPIFYKCLEILAQKILMNYDYERDEV   950
 951  YLMIFIKIFQKCVHSKLQFTDATLKLIVKITKFIEKVFIETKFSSLSGRQ  1000
1001  TFLKFIFQLSPTSHVYSKFDYQKLISLTLKDSDVCVIYNFVDDLVIFLKK  1050
1051  CDKTLIEGFVLPILSIKIEKSLYKGFCYLYLTLKVFLSISSNRSALLYQL  1100
1101  LKLANSYETSTIFEPLLRKLHIQSANIKQLFRIYRLEIFWSFVSKDLSNT  1150
1151  TNDFLEFPYKPIYFSLSDFLKENSDEIILVLILTKNITLAKLITSRMSVD  1200
1201  FSEKYTQLIPVITTYTHLSEVENKKYSLRFNSIDEALDVELLNRSKAFLF  1250
1251  CLEMLKEVKELGSTFKSISSTSFKVYSQLTIFANRVSFNNSTAIPFFSTK  1300
1301  SVLWYCNRLFQELEGFSSIPSVIDLVLRRLAIQLHFATDEELQVTISFRL  1350
1351  CAFLCFSDPFITSNYLVMIVLRIARQLLSIPCTQSLGLGIARFHLKKFKP  1400
1401  TDFDYFFQLAEFCMDFLGFCYNTIGTKMEAIQDFYTWFDGYVTALLNFEY  1450
1451  EGYGFLRCQINFVRSVMTTKNEWIEVSNKLFERGHFLKRIAMNNYLCLYF  1500
1501  WQVLDACPRNVLHSLSLEIWKCYKAYDITEFPDSLKLFFSDIMGWNFFKS  1550
1551  PEIADLNHYIPKTDPRLCDTKTYEESKLIIWKLICQKACSLLFKYDILLD  1600
1601  SFIEDCIRMFFENGNHQELRKFLNFPKDSIIYDSDFKTLVSEEGSFQWVK  1650
1651  LQPTNFDSLSNWTKEETLKLLNMMGKSSTTHSLKLLSTYMVGFSTSIIQY  1700
1701  IIHLILLEFDFNGNNKKQKEYVTQLILSGLLNKNTNSIRKTCMNILLYLR  1750
1751  RQLGHHALNPFEANYWVPINYSVAASTAYDCHLYEQSLLFLTIHNTKTDE  1800
1801  LDITLLSDILSQLPCPDAYYGIKRETSFKNILLKAVHEKRSPLAISYLDA  1850
1851  ANMYRSNEDEGTKMMFSNTLNNAGFFSLNEFYIDSLKANDAIDECSNEVY  1900
1901  ASAWRMQKWDIPPLSLDNKTTKDCLVFEVLHAVHNYAIYGNYLHLEEYIN  1950
1951  KKLLLINPNEEPDSLLFYALAYDLKFLIRCNQSQFNCDILQLLKENKQMS  2000
2001  SQLHECFQLLLEIRNVLLSLLQSHKQLDLSDDLASFRKYYILELLKISES  2050
2051  FLIVDNLQNAFSVAMLSDALYRKFDLADENLKHDIDFLSSKILWQRDEKI  2100
2101  DAIGMLSESLSKTNSSIFPSISYAYLGNWLYTTKSEKTELVSKNYFEKSL  2150
2151  SHMSHLNAKEKAKIYCMFAQFCDNNYSSPDLTEDFKRMEKLYFEKKNDIQ  2200
2201  QLERSIVNASNMKEEKMLKNHHSREMSSFIIDEREYLRMSTFRSKMLTQS  2250
2251  ITHYLKCLSESDENDVLISRCCTMWLSNSHLDELNNSLQHYLQNLPCKKF  2300
2301  IPVFYQLAARLMNENSKFQQSLTSICYNVGRNHPYHSLHVLFSLVSNVPE  2350
2351  IENLDAGSRYRAVKKILDLLKVNQGLSNLVTKLLCSFENYVSLAEWNPRS  2400
2401  KVDSTSFSRFPGYKWFLKDAANYGLPPITMNVKVNDTGDYSNIPTVSSFD  2450
2451  DTIHFASGINAPKVITCLGSNGHTYKQLVKGGNDDLRQDAVMEQVFEQVN  2500
2501  GFLRSYRKTSQRNLSMRTYKVIPLALKTGVIEWVQDTIPLGEYLDSAHKV  2550
2551  YHPKEWSLSTCRKLIAEKQMEDLETRLKVYDLVCRHYRPVFRHFFLESYA  2600
2601  DPVQWFTTQTNYARSTAVASVLGHVLGLGDRHGQNILIDKTSGEVIHIDL  2650
2651  GIAFEQGKKLPVPECVPFRLTRDVVDGMGITGVEGVFRRCMEFTLETLRR  2700
2701  EEDSLLSVLEVLRYDPLFSWLISPLRRMKKQKMQLENFNQPESGNITTDA  2750
2751  SRDPKIQRNNVSGESEAERAILKVRQKLSSTLSVEASVGELIRIAQDPSY  2800
2801  LALMFCGWSAFQ                                        2812

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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