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

NucPred

Fetching P02566 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MEHEKDPGWQYLRRTREQVLEDQSKPYDSKKNVWIPDPEEGYLAGEITAT    50
  51  KGDQVTIVTARGNEVTLKKELVQEMNPPKFEKTEDMSNLSFLNDASVLHN   100
 101  LRSRYAAMLIYTYSGLFCVVINPYKRLPIYTDSCARMFMGKRKTEMPPHL   150
 151  FAVSDEAYRNMLQDHENQSMLITGESGAGKTENTKKVICYFAAVGASQQE   200
 201  GGAEVDPNKKKVTLEDQIVQTNPVLEAFGNAKTVRNNNSSRFGKFIRIHF   250
 251  NKHGRLASCDIEHYLLEKSRVIRQAPGERCYHIFYQIYSDFRPELKKELL   300
 301  LDLPIKDYWFVAQAELIIDGIDDVEEFQLTDEAFDILNFSAVEKQDCYRL   350
 351  MSAHMHMGNMKFKQRPREEQAEPDGTDEAEKASNMYGIGCEEFLKALTKP   400
 401  RVKVGTEWVSKGQNCEQVNWAVGAMAKGLYSRVFNWLVKKCNLTLDQKGI   450
 451  DRDYFIGVLDIAGFEIFDFNSFEQLWINFVNEKLQQFFNHHMFVLEQEEY   500
 501  AREGIQWVFIDFGLDLQACIELIEKPLGIISMLDEECIVPKATDLTLASK   550
 551  LVDQHLGKHPNFEKPKPPKGKQGEAHFAMRHYAGTVRYNCLNWLEKNKDP   600
 601  LNDTVVSAMKQSKGNDLLVEIWQDYTTQEEAAAKAKEGGGGGKKKGKSGS   650
 651  FMTVSMLYRESLNNLMTMLNKTHPHFIRCIIPNEKKQSGMIDAALVLNQL   700
 701  TCNGVLEGIRICRKGFPNRTLHPDFVQRYAILAAKEAKSDDDKKKCAEAI   750
 751  MSKLVNDGSLSEEMFRIGLTKVFFKAGVLAHLEDIRDEKLATILTGFQSQ   800
 801  IRWHLGLKDRKRRMEQRAGLLIVQRNVRSWCTLRTWEWFKLYGKVKPMLK   850
 851  AGKEAEELEKINDKVKALEDSLAKEEKLRKELEESSAKLVEEKTSLFTNL   900
 901  ESTKTQLSDAEERLAKLEAQQKDASKQLSELNDQLADNEDRTADVQRAKK   950
 951  KIEAEVEALKKQIQDLEMSLRKAESEKQSKDHQIRSLQDEMQQQDEAIAK  1000
1001  LNKEKKHQEEINRKLMEDLQSEEDKGNHQNKVKAKLEQTLDDLEDSLERE  1050
1051  KRARADLDKQKRKVEGELKIAQENIDESGRQRHDLENNLKKKESELHSVS  1100
1101  SRLEDEQALVSKLQRQIKDGQSRISELEEELENERQSRSKADRAKSDLQR  1150
1151  ELEELGEKLDEQGGATAAQVEVNKKREAELAKLRRDLEEANMNHENQLGG  1200
1201  LRKKHTDAVAELTDQLDQLNKAKAKVEKDKAQAVRDAEDLAAQLDQETSG  1250
1251  KLNNEKLAKQFELQLTELQSKADEQSRQLQDFTSLKGRLHSENGDLVRQL  1300
1301  EDAESQVNQLTRLKSQLTSQLEEARRTADEEARERQTVAAQAKNYQHEAE  1350
1351  QLQESLEEEIEGKNEILRQLSKANADIQQWKARFEGEGLLKADELEDAKR  1400
1401  RQAQKINELQEALDAANSKNASLEKTKSRLVGDLDDAQVDVERANGVASA  1450
1451  LEKKQKGFDKIIDEWRKKTDDLAAELDGAQRDLRNTSTDLFKAKNAQEEL  1500
1501  AEVVEGLRRENKSLSQEIKDLTDQLGEGGRSVHEMQKIIRRLEIEKEELQ  1550
1551  HALDEAEAALEAEESKVLRAQVEVSQIRSEIEKRIQEKEEEFENTRKNHA  1600
1601  RALESMQASLETEAKGKAELLRIKKKLEGDINELEIALDHANKANADAQK  1650
1651  NLKRYQEQVRELQLQVEEEQRNGADTREQFFNAEKRATLLQSEKEELLVA  1700
1701  NEAAERARKQAEYEAADARDQANEANAQVSSLTSAKRKLEGEIQAIHADL  1750
1751  DETLNEYKAAEERSKKAIADATRLAEELRQEQEHSQHVDRLRKGLEQQLK  1800
1801  EIQVRLDEAEAAALKGGKKVIAKLEQRVRELESELDGEQRRFQDANKNLG  1850
1851  RADRRVRELQFQVDEDKKNFERLQDLIDKLQQKLKTQKKQVEEAEELANL  1900
1901  NLQKYKQLTHQLEDAEERADQAENSLSKMRSKSRASASVAPGLQSSASAA  1950
1951  VIRSPSRARASDF                                       1963

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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