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

NucPred

Fetching P34731 from www.uniprot.org...

The NucPred score for your sequence is 0.14 (see score help below)

   1  MSTHRPFQLTHGSIEHTLLVPNDLFFNYSQLKDEFIKTLPEPTEGFAGDD    50
  51  EPSSPAELYGKFIGFISNAQFPQIVELSLKDFESRFLDNNNDNIHSFAVK   100
 101  LLDDETYPTTIAKVKENIVKNYYKAVKSINKVESNLLYHCKHDAKLVAIF   150
 151  GGQGNTDDYFEELRELYTLYQGLIEDLLVSIAEKLNQLHPSFDKIYTQGL   200
 201  NILSWLKHPETTPDQDYLLSVPVSCPVICVIQLCHYTITCKVLGLTPGEF   250
 251  RNSLKWSTGHSQGLVTAVTIAASDSWDSFLKNSLTAVSLLLFIGSRCLST   300
 301  YPRTSLPPTMLQDSLDNGEGRPSPMLSVRDLSIKQVEKFIEQTNSHLPRE   350
 351  KHIAISLINGARNLVLSGPPESLYGFNLNLRNQKAPMGLDQSRVPFSERK   400
 401  LKCSNRFLPIFAPFHSHLLADATELILDDVKEHGLSFEGLKIPVYDTFDG   450
 451  SDFQALKEPIIDRVVKLITELPVHWEEATNHKATHILDFGPGGVSGLGVL   500
 501  THRNKEGTGARIILAGTLDSNPIDDEYGFKHEIFQTSADKAIKWAPDWLK   550
 551  ELRPTLVKNSEGKIYVKTKFSQLLGRAPLMVAGMTPTTVNTDIVSASLNA   600
 601  GYHIELAGGGYFSPVMMTRAIDDIVSRIKPGYGLGINLIYVNPFMLQWGI   650
 651  PLIKDLREKGYPIQSLTIGAGVPSIEVATEYIEDLGLTHLGLKPGSVDAI   700
 701  SQVIAIAKAHPTFPIVLQWTGGRGGGHHSFEDFHQPIIQMYSKIRRCSNI   750
 751  VLVAGSGFGSDEDTYPYLSGYWSEKFNYPPMPFDGVLFGSRVMTSKESHT   800
 801  SLAAKKLIVECKGVPDQQWEQTYKKPTGGIITVRSEMGEPIHKIATRGVM   850
 851  FWKELDDTIFNLPKNKLLDALNKKRDHIIKKLNNDFQKPWFGKNANGVCD   900
 901  LQEMTYKEVANRLVELMYVKKSHRWIDVSLRNMYGDFLRRVEERFTSSAG   950
 951  TVSLLQNFNQLNEPEQFTADFFEKFPQAGKQLISEEDCDYFLMLAARPGQ  1000
1001  KPVPFVPVLDERFEFFFKKDSLWQSEDLESVVDEDVQRTCILHGPVASQY  1050
1051  TSKVDEPIGDILNSIHEGHIARLIKEEYAGDESKIPVVEYFGGKKPASVS  1100
1101  ATSVNIIDGNQVVYEIDSELPNKQEWLDLLAGTELNWLQAFISTDRIVQG  1150
1151  SKHVSNPLHDILTPAKHSKVTIDKKTKKLTAFENIKGDLLPVVEIELVKP  1200
1201  NTIQLSLIEHRTADTNPVALPFLYKYNPADGFAPILEIMEDRNERIKEFY  1250
1251  WKLWFGSSVPYSNDINVEKAILGDEITISSQTISEFTHAIGNKCDAFVDR  1300
1301  PGKATLAPMDFAIVIGWKAIIKAIFPKSVDGDLLKLVHLSNGYKMITGAA  1350
1351  PLKKGDVVSTKAEIKAVLNQPSGKLVEVVGTIYREGKPVMEVTSQFLYRG  1400
1401  EYNDYCNTFQKVTETPVQVAFKSAKDLAVLRSKEWFHLEKDVQFDVLTFR  1450
1451  CESTYKFKSANVYSSIKTTGQVLLELPTKEVIQVGSVDYEAGTSYGNPVT  1500
1501  DYLSRNGKTIEESVIFENAIPLSSGEELTSKAPGTNEPYAIVSGDYNPIH  1550
1551  VSRVFAAYAKLPGTITHGMYSSASIRALVEEWAANNVAARVRAFKCDFVG  1600
1601  MVLPNDTLQTTMEHVGMINGRKIIKVETRNVETELPVLIGEAEIEQPTTT  1650
1651  YVFTGQGSQEQGMGMELYNSSEVAREVWDKADRHFVNNYGFSILDIVQNN  1700
1701  PNELTIHFGGAKGRAIRDNYIGMMFETIGEDGALKSEKIFKDIDETTTSY  1750
1751  TFVSPTGLLSATQFTQPALTLMEKAAYEDIKSKGLIPSDIMFAGHSLGEY  1800
1801  SALSSLANVMPIESLVDVVFYRGMTMQVAVPRDELGRSNYGMVAVNPSRV  1850
1851  SATFDDSALRFVVDEVANKTKWLLEIVNYNVENQQYVAAGDLRALDTLTN  1900
1901  VLNVLKINKIDIVKLQEQMSIEKVKEHLYEIVDEVAAKSLAKPQPIDLER  1950
1951  GFAVIPLKGISVPFHSSYLMSGVKPFQRFLCKKIPKSSVKPQDLIGKYIP  2000
2001  NLTAKPFELTKEYFQSVYDLTKSEKIKSILDNWEQYE               2037

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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