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

NucPred

Fetching P50077 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MQGRKRTLTEPFEPNTNPFGDNAAVMTENVEDNSETDGNRLESKPQALVP    50
  51  PALNIVPPESSIHSTEEKKGDEYNGNDKDSSLISNIFRTRVGRSSHENLS   100
 101  RPKLSLKTASFGAAESSRRNVSPSTKSAKSSSQYIDLNDERLRRRSFSSY   150
 151  SRSSSRRVSNSPSSTDRPPRSAKVLSLIAADDMDDFEDLQKGFKSAIDEE   200
 201  GLTWLPQLKSEKSRPVSDVGEDRGEGEQESIPDVHTPNVGASATPGSIHL   250
 251  TPEPAQNGSVSEGLEGSINNSRKKPSPKFFHHLSPQKEDKDQTEVIEYAE   300
 301  DILDFETLQRKLESRPFVLYGHSLGVFSPTNPLRIKIARFLLHRRYSLLY   350
 351  NTLLTFYAILLAIRTYNPHNVVFLYRFSNWTDYFIFILSACFTGNDIAKI   400
 401  IAFGFWDDSEMFKAYGREYKSILQRSGIMKLYIYLREKYGRKLIDFIIPF   450
 451  RIISPGEETKYQRSSLSTSLTKPYGAKENQRPFGTPRAFARSSWNRIDLV   500
 501  SSVSFWLGMFLSIKSYDTKTGIRIFKPLAILRILRLVNVDTGMPSILRGL   550
 551  KYGIPQLVNVSSMLVYFWIFFGILGVQIFQGSFRRQCVWFNPEDPTDTYQ   600
 601  YDMQFCGGYLDPVTKRKQNYIYEDGSEGSVSKGFLCPQYSKCVSNANPYN   650
 651  GRISFDNIVNSMELVFVIMSANTFTDLMYYTMDSDEMAACLFFIVCIFVL   700
 701  TIWLLNLLIAVLVSSFEIANEEYKKKKFIYGSRKTGYVARIVTGYWKYFK   750
 751  LKANQTKFPNWSQKGLAIYSHVEFIFVILIICDIGMRASVKVSTSANCNN   800
 801  ILLKTDRGISIVLFIESLARLVLYLPNMWKFLTKPSYVYDFIISIITLVI   850
 851  SCLAVEGVLGHMYAWLSIFHISRFYRVIISFNLTKKLWKQILSNGVMIWN   900
 901  LSSFYFFFTFLVAIIMAVYFEGVIPPEEMADQPFGMYSLPNSFLSLFIIG   950
 951  STENWTDILYALQKHSPNISSTFFCSVFFIIWFLLSNSVILNIFIALISE  1000
1001  SMEVKEEEKRPQQIKHYLKFVYPQKIQEYTHASLVARIRKKFFGGHRNED  1050
1051  TRDFKQFLMRGTAIMNIAQNMGELADEFKEPPSENLFKKGLSKLTIGVPS  1100
1101  LKRLRMFANNPFYKNSDVVFTETNDINGRTYILELNEYEDEKLDYLKKYP  1150
1151  LFNYSYYFFSPQHRFRRFCQRLVPPSTGKRTDGSRFFEDSTDLYNKRSYF  1200
1201  HHIERDVFVFIFALATILLIVCSCYVTPLYRMHHKMGTWNWSSALDCAFI  1250
1251  GAFSIEFIVKTVADGFIYSPNAYLRNPWNFIDFCVLISMWINLIAYLKNN  1300
1301  GNLSRIFKGLTALRALRCLTISNTARQTFNLVMFDGLNKIFEAGLISLSL  1350
1351  LFPFTVWGLSIFKGRLGTCNDGSLGRADCYNEYSNSVFQWDIMSPRVYQQ  1400
1401  PYLHLDSFASAFSSLYQIISLEGWVDLLENMMNSSGIGTPATVMGSAGNA  1450
1451  LFLVLFNFLSMVFILNLFVSFIVNNQARTTGSAYFTIEEKAWLESQKLLS  1500
1501  QAKPKAIPNLIELSRVRQFFYQLAVEKKNFYYASFLQVVLYLHIIMLLSR  1550
1551  SYNPGNLIGYQGVYFMFSTSVFLIQEALHMCGEGPRLYFRQKWNSIRLSI  1600
1601  IIIAFIMNAVAFHVPASHYWFHNIKGFFLLVIFLFIIPQNDTLTELLETA  1650
1651  MASLPPILSLTYTWGVLFLVYAIALNQIFGLTRLGSNTTDNINFRTVIKS  1700
1701  MIVLFRCSFGEGWNYIMADLTVSEPYCSSDDNSTYTDCGSETYAYLLLMS  1750
1751  WNIISMYIFVNMFVSLIIGNFSYVYRSGGSRSGINRSEIKKYIEAWSKFD  1800
1801  TDGTGELELSYLPRIMHSFDGPLSFKIWEGRLTIKSLVENYMEVNPDDPY  1850
1851  DVKIDLIGLNKELNTIDKAKIIQRKLQYRRFVQSIHYTNAYNGCIRFSDL  1900
1901  LLQIPLYTAYSARECLGIDQYVHHLYILGKVDKYLENQRNFDVLEMVVTR  1950
1951  WKFHCRMKRTIEPEWDVKDPTVSSHISNINVNLEPAPGILEREPIATPRM  2000
2001  DYGVNNFMWSPRMNQDSTMEPPEEPIDNNDDSANDLIDR             2039

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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