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

NucPred

Fetching Q9EQ60 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MTEGTLAADEVRVPLGASPPAPAAPVRASPASPGAPGREEQGGSGSGVLA    50
  51  PESPGTECGADLGADEEQPVPYPALAATVFFCLGQTTRPRSWCLRLVCNP   100
 101  WFEHISMLVIMLNCVTLGMFRPCEDVECRSERCSILEAFDDFIFAFFAVE   150
 151  MVIKMVALGLFGQKCYLGDTWNRLDFFIVMAGMMEYSLDGHNVSLSAIRT   200
 201  VRVLRPLRAINRVPSMRILVTLLLDTLPMLGNVLLLCFFVFFIFGIVGVQ   250
 251  LWAGLLRNRCFLDSAFVRNNNLTFLRPYYQTEEGEENPFICSSRRDNGMQ   300
 301  KCSHIPSRRELRVQCTLGWEAYGQPQAEDGGAGRNACINWNQYYNVCRSG   350
 351  EFNPHNGAINFDNIGYAWIAIFQVITLEGWVDIMYYVMDAHSFYNFIYFI   400
 401  LLIIMGSFFMINLCLVVIATQFSETKQRENQLMREQRARYLSNDSTLASF   450
 451  SEPGSCYEELLKYVGHIFRKVKRRSLRLYARWQSRWRKKVDPSSTVHGQG   500
 501  PGRRPRRAGRRTASVHHLVYHHHHHHHHHYHFSHGGPRRPSPEPGAGDNR   550
 551  LVRACAPPSPPSPGHGPPDSESVHSIYHADCHVEGPQERARVAHSIATAA   600
 601  SLKLASGLGTMNYPTILPSGTVNSKGGTSSRPKGLRGAGAPGAAVHSPLS   650
 651  LGSPRPYEKIQDVVGEQGLGRASSHLSGLSVPCPLPSPQAGTLTCELKSC   700
 701  PYCASALEDPEFEFSGSESGDSDAHGVYEFTQDVRHGDCRDPVQQPHEVG   750
 751  TPGHSNERRRTPLRKASQPGGIGHLWASFSGKLRRIVDSKYFNRGIMAAI   800
 801  LVNTLSMGVEYHEQPEELTNALEISNIVFTSMFALEMLLKLLACGPLGYI   850
 851  RNPYNIFDGIVVVISVWEIVGQANGGLSVLRTFRLLRVLKLVRFLPALRR   900
 901  QLVVLMRTMDNVATFCMLLMLFIFIFSILGMHLFGCKFSLKTDSGDTVPD   950
 951  RKNFDSLLWAIVTVFQILTQEDWNVVLYNGMASTSSWAALYFVALMTFGN  1000
1001  YVLFNLLVAILVEGFQAEGDATRSDTDEDKTSTQLEGDFDKLRDLRATEM  1050
1051  KMYSLAVTPNGHLEGRGSLPPPLITHTAATPMPTPKSSPNLDVAHALLDS  1100
1101  RRSSSGSVDPQLGDQKSLASLRSSPCTPWGPNSAGSSRRSSWNSLGRAPS  1150
1151  LKRRNQCGERESLLSGEGKGSTDDEAEDSRPSTGTHPGASPGPRATPLRR  1200
1201  AESLDHRSTLDLCPPRPAALLPTKFHDCNGQMVALPSEFFLRIDSHKEDA  1250
1251  AEFDDDIEDSCCFRLHKVLEPYAPQWCRSRESWALYLFPPQNRLRVSCQK  1300
1301  VIAHKMFDHVVLVFIFLNCITIALERPDIDPGSTERAFLSVSNYIFTAIF  1350
1351  VVEMMVKVVALGLLWGEHAYLQSSWNVLDGLLVLVSLVDIIVAMASAGGA  1400
1401  KILGVLRVLRLLRTLRPLRVISRAPGLKLVVETLISSLRPIGNIVLICCA  1450
1451  FFIIFGILGVQLFKGKFYYCEGTDTRNITTKAECHAAHYRWVRRKYNFDN  1500
1501  LGQALMSLFVLSSKDGWVNIMYDGLDAVGIDQQPVQNHNPWMLLYFISFL  1550
1551  LIVSFFVLNMFVGVVVENFHKCRQHQEAEEARRREEKRLRRLERRRRKAQ  1600
1601  RRPYYADYSHTRRSIHSLCTSHYLDLFITFIICLNVITMSMEHYNQPKSL  1650
1651  DEALKYCNYVFTIVFVFEAALKLVAFGFRRFFKDRWNQLDLAIVLLSIMG  1700
1701  IALEEIEMNAALPINPTIIRIMRVLRIARVLKLLKMATGMRALLDTVVQA  1750
1751  LPQVGNLGLLFMLLFFIYAALGVELFGRLECSEDNPCEGLSRHATFTNFG  1800
1801  MAFLTLFRVSTGDNWNGIMKDTLRECTREDKHCLSYLPALSPVYFVTFML  1850
1851  VAQFVLVNVVVAVLMKHLEESNKEAREDAEMDAEIELEMAQGSTAQPPPT  1900
1901  AQESQGTQPDTPNLLVVRKVSVSRMLSLPNDSYMFRPVAPAAAPHSHPLQ  1950
1951  EVEMETYTGPVTSAHSPPLEPRASFQVPSAASSPARVSDPLCALSPRGTP  2000
2001  RSLSLSRILCRQEAMHSESLEGKVDDVGGDSIPDYTEPAENMSTSQASTG  2050
2051  APRSPPCSPRPASVRTRKHTFGQRCISSRPPTLGGDEAEAADPADEEVSH  2100
2101  ITSSAHPWPATEPHSPEASPTASPVKGTMGSGRDPRRFCSVDAQSFLDKP  2150
2151  GRPDAQRWSSVELDNGESHLESGEVRGRASELEPALGSRRKKKMSPPCIS  2200
2201  IEPPTKDEGSSRPPAAEGGNTTLRRRTPSCEAALHRDCPEPTEGPGTGGD  2250
2251  PVAKGERWGQASCRAEHLTVPNFAFEPLDMGGPGGDCFLDSDQSVTPEPR  2300
2301  VSSLGAIVPLILETELSMPSGDCPEKEQGLYLTVPQTPLKKPGSTPATPA  2350
2351  PDDSGDEPV                                           2359

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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