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

NucPred

Fetching P39960 from www.uniprot.org...

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

   1  MKGLLWSKNRKSSTASASSSSTSTSHKTTTASTASSSSPSSSSQTIRNST    50
  51  SGASPYMHSHHHHGQGHSHHRGEDNNRDKRKSSVFPPSKQYTSTSSSQVN   100
 101  LGMYHSDTNTRSSRSIASTLKDDSPSVCSEDEISNSSSQKSNAQDETPIA   150
 151  YKKSAHSKDSLLPSRSSSLSPPQSRCSTGTTLEKSLNTSGISNSSGTNNN   200
 201  NSNNNNDNEQKQRNVIHLNSENYDTTVFKTGWVNKSHGQTVATNYNSSMT   250
 251  APSSSSSSSSQNLRNDAYSRNRESRFYGNDGSSLKNDDSSSTTATNSGND   300
 301  VASARSSMAIDPQMLVPDYRLYRAQLKGCVLNLYKSGLNSNIKFFDPTLP   350
 351  ASNSSIANENHQQKKQQTNNQAQAEALHQKQSFGQMGEPITLDLKYLSEV   400
 401  YPHPDLRQDSDGKIISGTIESLCHTVLFYPGPKQSDVPNEKSLSKTHRAV   450
 451  INLLLMFPLLDHFIKFLKVFNQFGLSFTKNKSRLTNNSTQFYNISPAVDD   500
 501  SMTQRLALTAKTILDVFPGFLLDEPMLKTIISLLDTISLHNDEISNNLKI   550
 551  KIANKHNELMKLTAFTRSLPMATSSTHELEIILDPSHFLSLDITTLADEV   600
 601  HHINLKFDKVWAPKFDYSLLYDSKFINRRIVSLNPLVFNNDQNIHFLGRL   650
 651  LISHLFPTNPEFSKKVTPKVRAELLDKWVQIGCRFEHLGDMVSWLAVATI   700
 701  ICSIPVLRSSSWKYVPDQSLKTIFKDWVPTIIQLERRQRTSKSTSSVFIL   750
 751  APPNLDDDFTRANVISYFGDLLIHADDLPSDTKFKYLEKKINRTKNAFHK   800
 801  WQQRLQAIDSTRHKTNSTENVRDNDSPNNVVYQLWKFHLSQPPLNIEGIM   850
 851  KLSVQHEPPIIDQKAYSTIGSQRSALVTGSYLPILFNELFPNYSLFPKNT   900
 901  LVGAASDAKLPPPRSSARLSKSLSISEPIPIASNSHTMGSLTDDAMSSKN   950
 951  DNNKVTGVGKIDGPVIKEMSSKQSNKQRLLKSVRDVFNIDMDVFHISDEL  1000
1001  VFKSVYDNDGKSRPASMVIETPKRFSQHSSMLINNPATPNQKMRDSLDTT  1050
1051  GRLSKTLENMDFFNNIGQVSDSLKESIIRVVLKSSSLEKIFDLLVLTSNI  1100
1101  FSKLVDTKDLENYYYHQRQRGHSTRGLSDDNIGLLDYAFVKLTMDNDIFT  1150
1151  ETFFNTYKSFTTTTTVLENMAKRYVGAKSCSVSISKILDRSDDSKMKINE  1200
1201  DTNLVSSSLYDQNFPVWDMKVTDDENINLIYMAKIQIGAAEAILHLVKNH  1250
1251  YSDFTDDLCNNSTLLDIIKIMEQEVSTEWPTRIANSKLQKSLPENFVIET  1300
1301  ENLLTTLTDLFHGIKSAYQKQLYRPIGVNRTQKRITDILNSFNTFSFTDL  1350
1351  NNIIDDPSFSDDMIRSFQKLHSTNYEDILEWIYQLDNFISKKFNLVSKKD  1400
1401  WIVLFQELELLSKESLVSFFNYPLHFKSSKLINPGYLQLHEFEISNLFTW  1450
1451  ISTLILKDDNGTESLFFEKLPQSIKLLIKLHTSLTTFFVMEISNVNKSSS  1500
1501  ERLTTCKVILQILNYIRWKNGSLDLFDSEEDESPHAICPHIPAFIETAIA  1550
1551  HAIISPESRNYELSWIKASEKLSDPTKGTQNLRSISNVLEKIDDIHIKRF  1600
1601  IEIDDVFSKNCKNLCPCPGWFISRLLEISQFVPNMSITNSKLINFDKRRF  1650
1651  VNNIISNVLDLIPNEREFPLDIEMSDENPSKRTTFGRILFNNFEDVNKVY  1700
1701  RKKTKKVSESEAISERFQEQGVFNEILVNEIEKIKREARKLEVLLDQEKI  1750
1751  LKNSAALHQAVPKKNRKSVIISGTHSDNDHSYNINKNTGQTPSLGSVMES  1800
1801  NNSARNRRDSRASFSTNRSSVVSNSSHNGVSKKIGGFFRRPFSIGGFNTS  1850
1851  SSNYSLNSILSQEVSSNKSILPSILPEVDSMQLHDLKPSYSLKTFEIKSI  1900
1901  MEIINHRNIPAYYYAFKIVMQNGHEYLIQTASSSDLTEWIKMIKASKRFS  1950
1951  FHSKKYKGKTHNKIFGVPLEDVCERENTLIPTIVVKLLEEIELRGLDEVG  2000
2001  LYRIPGSIGSINALKNAFDEEGATDNSFTLEDDRWFEVNAIAGCFKMYLR  2050
2051  ELPDSLFSHAMVNDFTDLAIKYKAHAMVNEEYKRMMNELLQKLPTCYYQT  2100
2101  LKRIVFHLNKVHQHVVNNKMDASNLAIVFSMSFINQEDLANSMGSRLGAV  2150
2151  QTILQDFIKNPNDYFKQ                                   2167

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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