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

NucPred

Fetching Q99973 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MEKLHGHVSAHPDILSLENRCLAMLPDLQPLEKLHQHVSTHSDILSLKNQ    50
  51  CLATLPDLKTMEKPHGYVSAHPDILSLENQCLATLSDLKTMEKPHGHVSA   100
 101  HPDILSLENRCLATLSSLKSTVSASPLFQSLQISHMTQADLYRVNNSNCL   150
 151  LSEPPSWRAQHFSKGLDLSTCPIALKSISATETAQEATLGRWFDSEEKKG   200
 201  AETQMPSYSLSLGEEEEVEDLAVKLTSGDSESHPEPTDHVLQEKKMALLS   250
 251  LLCSTLVSEVNMNNTSDPTLAAIFEICRELALLEPEFILKASLYARQQLN   300
 301  VRNVANNILAIAAFLPACRPHLRRYFCAIVQLPSDWIQVAELYQSLAEGD   350
 351  KNKLVPLPACLRTAMTDKFAQFDEYQLAKYNPRKHRAKRHPRRPPRSPGM   400
 401  EPPFSHRCFPRYIGFLREEQRKFEKAGDTVSEKKNPPRFTLKKLVQRLHI   450
 451  HKPAQHVQALLGYRYPSNLQLFSRSRLPGPWDSSRAGKRMKLSRPETWER   500
 501  ELSLRGNKASVWEELIENGKLPFMAMLRNLCNLLRVGISSRHHELILQRL   550
 551  QHAKSVIHSRQFPFRFLNAHDAIDALEAQLRNQALPFPSNITLMRRILTR   600
 601  NEKNRPRRRFLCHLSRQQLRMAMRIPVLYEQLKREKLRVHKARQWKYDGE   650
 651  MLNRYRQALETAVNLSVKHSLPLLPGRTVLVYLTDANADRLCPKSNPQGP   700
 701  PLNYALLLIGMMITRAEQVDVVLCGGDTLKTAVLKAEEGILKTAIKLQAQ   750
 751  VQEFDENDGWSLNTFGKYLLSLAGQRVPVDRVILLGQSMDDGMINVAKQL   800
 801  YWQRVNSKCLFVGILLRRVQYLSTDLNPNDVTLSGCTDAILKFIAEHGAS   850
 851  HLLEHVGQMDKIFKIPPPPGKTGVQSLRPLEEDTPSPLAPVSQQGWRSIR   900
 901  LFISSTFRDMHGERDLLLRSVLPALQARAAPHRISLHGIDLRWGVTEEET   950
 951  RRNRQLEVCLGEVENAQLFVGILGSRYGYIPPSYNLPDHPHFHWAQQYPS  1000
1001  GRSVTEMEVMQFLNRNQRLQPSAQALIYFRDSSFLSSVPDAWKSDFVSES  1050
1051  EEAARRISELKSYLSRQKGITCRRYPCEWGGVAAGRPYVGGLEEFGQLVL  1100
1101  QDVWNMIQKLYLQPGALLEQPVSIPDDDLVQATFQQLQKPPSPARPRLLQ  1150
1151  DTVQRLMLPHGRLSLVTGQSGQGKTAFLASLVSALQAPDGAKVASLVFFH  1200
1201  FSGARPDQGLALTLLRRLCTYLRGQLKEPGALPSTYRSLVWELQQRLLPK  1250
1251  SAESLHPGQTQVLIIDGADRLVDQNGQLISDWIPKKLPRCVHLVLSVSSD  1300
1301  AGLGETLEQSQGAHVLALGPLEASARARLVREELALYGKRLEESPFNNQM  1350
1351  RLLLVKRESGRPLYLRLVTDHLRLFTLYEQVSERLRTLPATVPLLLQHIL  1400
1401  STLEKEHGPDVLPQALTALEVTRSGLTVDQLHGVLSVWRTLPKGTKSWEE  1450
1451  AVAAGNSGDPYPMGPFACLVQSLRSLLGEGPLERPGARLCLPDGPLRTAA  1500
1501  KRCYGKRPGLEDTAHILIAAQLWKTCDADASGTFRSCPPEALGDLPYHLL  1550
1551  QSGNRGLLSKFLTNLHVVAAHLELGLVSRLLEAHALYASSVPKEEQKLPE  1600
1601  ADVAVFRTFLRQQASILSQYPRLLPQQAANQPLDSPLCHQASLLSRRWHL  1650
1651  QHTLRWLNKPRTMKNQQSSSLSLAVSSSPTAVAFSTNGQRAAVGTANGTV  1700
1701  YLLDLRTWQEEKSVVSGCDGISACLFLSDDTLFLTAFDGLLELWDLQHGC  1750
1751  RVLQTKAHQYQITGCCLSPDCRLLATVCLGGCLKLWDTVRGQLAFQHTYP  1800
1801  KSLNCVAFHPEGQVIATGSWAGSISFFQVDGLKVTKDLGAPGASIRTLAF  1850
1851  NVPGGVVAVGRLDSMVELWAWREGARLAAFPAHHGFVAAALFLHAGCQLL  1900
1901  TAGEDGKVQVWSGSLGRPRGHLGSLSLSPALSVALSPDGDRVAVGYRADG  1950
1951  IRIYKISSGSQGAQGQALDVAVSALAWLSPKVLVSGAEDGSLQGWALKEC  2000
2001  SLQSLWLLSRFQKPVLGLATSQELLASASEDFTVQLWPRQLLTRPHKAED  2050
2051  FPCGTELRGHEGPVSCCSFSTDGGSLATGGRDRSLLCWDVRTPKTPVLIH  2100
2101  SFPACHRDWVTGCAWTKDNLLISCSSDGSVGLWDPESGQRLGQFLGHQSA  2150
2151  VSAVAAVEEHVVSVSRDGTLKVWDHQGVELTSIPAHSGPISHCAAAMEPR  2200
2201  AAGQPGSELLVVTVGLDGATRLWHPLLVCQTHTLLGHSGPVRAAAVSETS  2250
2251  GLMLTASEDGSVRLWQVPKEADDTCIPRSSAAVTAVAWAPDGSMAVSGNQ  2300
2301  AGELILWQEAKAVATAQAPGHIGALIWSSAHTFFVLSADEKISEWQVKLR  2350
2351  KGSAPGNLSLHLNRILQEDLGVLTSLDWAPDGHFLILAKADLKLLCMKPG  2400
2401  DAPSEIWSSYTENPMILSTHKEYGIFVLQPKDPGVLSFLRQKESGEFEER  2450
2451  LNFDINLENPSRTLISITQAKPESESSFLCASSDGILWNLAKCSPEGEWT  2500
2501  TGNMWQKKANTPETQTPGTDPSTCRESDASMDSDASMDSEPTPHLKTRQR  2550
2551  RKIHSGSVTALHVLPELLVTASKDRDVKLWERPSMQLLGLFRCEGSVSCL  2600
2601  EPWLGANSTLQLAVGDVQGNVYFLNWE                         2627

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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