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

NucPred

Fetching Q9WV48 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MTHSPATSEDEERHSASECPEGGSESDSSPDGPGRGPQGTRGRGSGAPGN    50
  51  LASTRGLQGRSMSVPDDAHFSMMVFRIGIPDLHQTKCLRFNPDATIWTAK   100
 101  QQVLCALSESLQDVLNYGLFQPATSGRDANFLEEERLLREYPQSFEKGVP   150
 151  YLEFRYKTRVYKQTNLDEKQLAKLHTKTGLKKFLEYVQLGTSDKVARLLD   200
 201  KGLDPNYHDSDSGETPLTLAAQTEGSVEVIRTLCLGGAHIDFRARDGMTA   250
 251  LHKAACARHCLALTALLDLGGSPNYKDRRGLTPLFHTAMVGGDPRCCELL   300
 301  LYNRAQLGIADENGWQEIHQACQRGHSQHLEHLLFYGAEPGAQNASGNTA   350
 351  LHICALYNKETCARILLYRGANKDVKNNNGQTPFQVAVIAGNFELGELIR   400
 401  NHREQDVVPFQESPKYAARRRGPPGAGLTVPPALLRANSDTSMALPDWMV   450
 451  FSAPGASSSGTPGPTSGPQGQSQPSAPSTKLSSGTLRSASSPRGARARSP   500
 501  SRGRHPEDAKRQPRGRPSSSGTPRDGPAGGTGGSGGPGGSLGSRGRRRKL   550
 551  YSAVPGRSFMAVKSYQAQGEGEISLSKGEKIKVLSIGEGGFWEGQVKGRV   600
 601  GWFPSDCLEEVANRSQEGRQESRSDKAKRLFRHYTVGSYDSFDAPSLIDG   650
 651  IDSGSDYIIKEKTVLLQKKDSEGFGFVLRGAKAQTPIEEFTPTPAFPALQ   700
 701  YLESVDEGGVAWRAGLRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLM   750
 751  VKVVMVTRHPDMDEAVHKKASQQAKRLPPPAISLRSKSMTSELEEMVSPW   800
 801  KKKIEYEQQPAAVPSMEKKRTVYQMALNKLDEILAAAQQTISASESPGPG   850
 851  GLASLGKHRPKGFFATESSFDPHHRSQPSYDRPSFLPPGPGLMLRQKSIG   900
 901  AAEDDRPYLAPPAMKFSRSLSVPGSEDIPPPPTTSPPEPPYSTPPAPSSS   950
 951  GRLTPSPRGGPFNPSSGGPLPASSPSSFDGPSPPDTRGGGREKSLYHSAA  1000
1001  LPPAHHHPPHHHHHHAPPPQPHHHHAHPPHPPEMETGGSPDDPPPRLALG  1050
1051  PQPSLRGWRGGGPSPTSGAPSPSHHSSSGGSSGPTQAPALRYFQLPPRAA  1100
1101  SAAMYVPARSGRGRKGPLVKQTKVEGEPQKGSIPSASSPTSPALPRSEPP  1150
1151  PAGPSEKNSIPIPTIIIKAPSTSSSGRSSQGSSTEAEPPTQPDGAGGGGS  1200
1201  SPSPAPATSPVPPSPSPVPTPASPSGPATLDFTSQFGAALVGAARREGGW  1250
1251  QNEARRRSTLFLSTDAGDEDGGDSGLGPGGPPGPRLRHSKSIDEGMFSAE  1300
1301  PYLRLESGGSSGGYGAYAAGSRAYGGSGSSSAFTSFLPPRPLVHPLTGKA  1350
1351  LDPASPLGLALAARERALKESSEGGGTPQPPPRPPSPRYDAPPPTLHHHS  1400
1401  PHSPHSPHARHEPVLRLWGDPARRELGYRAGLGSQEKALTASPPAARRSL  1450
1451  LHRLPPTAPGVGPLLLQLGPEPPTPHPGVSKAWRTAAPEEPERLPLHVRF  1500
1501  LENCQARPPPAGTRGSSTEDGPGVPPPSPRRVLPTSPTSPRGNEENGLPL  1550
1551  LVLPPPAPSVDVDDGEFLFAEPLPPPLEFSNSFEKPESPLTPGPPHPLPD  1600
1601  PPSPATPLPAAPPPAVAAAPPTLDSTASSLTSYDSEVATLTQGAPAAPGD  1650
1651  PPAPGPPAPAAPAPPAPQPGPDPPPGTDSGIEEVDSRSSSDHPLETISSA  1700
1701  STLSSLSAEGGGNTGGVAGGGAGVASGTELLDTYVAYLDGQAFGGSGTPG  1750
1751  PPYPPQLMTPSKLRGRALGTSGNLRPGPSGGLRDPVTPTSPTVSVTGAGT  1800
1801  DGLLALSACPGPSTAGVAGGPVAVEPEVPPVPLPAASSLPRKLLPWEEGP  1850
1851  GPPPPPLPGPLSQPQASALATVKASIISELSSKLQQFGGSSTAGGALPWA  1900
1901  RGGSGGSTDSHHGGASYIPERTSSLQRQRLSEDSQTSLLSKPSSSIFQNW  1950
1951  PKPPLPPLPTGSGVSSSTAAAPGATSPSASSASASTRHLQGVEFEMRPPL  2000
2001  LRRAPSPSLLPASDHKVSPAPRPSSLPILPSGPIYPGLFDIRSSPTGGAG  2050
2051  GSTDPFAPVFVPPHPGISGGLGGALSGASRSLSPTRLLSLPPDKPFGAKP  2100
2101  LGFWTKFDVADWLEWLGLSEHRAQFLDHEIDGSHLPALTKEDYVDLGVTR  2150
2151  VGHRMNIDRALKFFLER                                   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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