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

NucPred

Fetching P27715 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MDDVGDYNDDQLSDGMSMRLLCITIKKARLQGAVDEFNSYVTVKLQTVKS    50
  51  TTVAVRGNLPCWEQEFIFETNRPDDGMVLELWAKGVLWDKLIGVHYMPLS   100
 101  EIRYSNAAGSGQWLQMDHELETRNGQTVGTRGPTGHNLLTDVRFELPFDV   150
 151  QGHDEDIQSRLLALNGLIEHDQLGPNNHHRAPFNHSGLSEDSDYTSDVSV   200
 201  PVNHHQLHPNSSAHQYESHLHPHRTRQLLHTREGAASYEDEEDAYHARHQ   250
 251  PESDDYNHQDTYDQHSSYYNDEYAPSGSSSQYQRQGYQDQDQQHQNIYED   300
 301  TVTPVREFGESAVPPAASSSRRQFDQVYGYASSSEERYDTPMSSGRLPRD   350
 351  EPILEHSEPEYVYDQNGYPEEDNYGINPTYSEDHFEGQTNDYSTTHQEPN   400
 401  DFRNDYNSSYQREYWNESEPLSYNSRPPNGHIRTGANTWREPSTSSRPTS   450
 451  SQAWNYQDDTHQYDEVDRGSRVSFTRTPSVDRTDRPSESGGGFYDEMSES   500
 501  GRPGRPDSHHNWRYDSIQEEDNEKDNWKQHVEGYEEGQEEKQKDNQKPND   550
 551  HSAASPQDHYHRSDSTAQQDFGNNIVRQTIQEEEEKRNYQELWHNAYKRV   600
 601  CADLGIKSSQASLVATTGGTLLQNLFLYRPKLAPAGHGATASQFQSPAGA   650
 651  TRFYANHNNNNNNVSKNELDSTTETPPDPSRTPSTSSMNPVPSLAVPMSP   700
 701  GPYLNSDPPSPVSPNPQIKRSIYRIKESYEDRNGGRERIYTTNLVSVYLE   750
 751  KMKPPDELEEGSSGSMRETQNEIKNGTQLHNAESNIFFPQDSVPKSISYN   800
 801  AGNLKNTSITTSKTSSAITNHSSLPPQPPSKPASRDSDPMKQLLTFSKSF   850
 851  KKVRRVRSAMPRRRKRKRVKIKKSRSCPILWKTEKTPHPMKSKSMTCIRI   900
 901  PKKTVIAPLRKEIKIVRMKPPAARCESDSKAHKKKNLLDVYKDMGKSTVL   950
 951  DGNGSSAANAFYKSIDAAPNMNVARTKTSIPLVSELVLKTMATKRAQAGL  1000
1001  ANAARTTFSDTELKTHVYKKTLQALIYPISATTPHNFATTTFQTPTFCYE  1050
1051  CEGLLWGLARQGLRCTQCQVKVHDKCRELLSADCLQRAAEKSTKHGEADR  1100
1101  TQSLVNVIRDRMKIQEQNKPEVFQMIRTVFDVDENIQKETLKTVKASILE  1150
1151  GSSKWSAKITLTVLCAQGLIAKDKTGKSDPYVTAQVGKTKRRTRTIHQEL  1200
1201  NPVWNEKFHFECHNSTDRIKVRVWDEDNDLKSKLRQKLTRESDDFLGQTV  1250
1251  IEVRTLSGEMDVWYNLEKRTDKSAVSGAIRLHINVEIKGEEKLAPYHVQY  1300
1301  TCLHEHLFAAHCVDEEVKLPKVRGEDSWKVCFQETGQEIAEEFAMRYGIE  1350
1351  SIYQAMTHFACLCTRYMCAGVPAVLSTLLANINAYYAHTTATSAVSAPDR  1400
1401  FAASNFGKERFVKLLDQLHNSLRIDLSAYRNHFPSSSPAKLQDLKSTVDL  1450
1451  LTSITFFRMKVLELASPPRASTVVRECAKACMQQTYQLMFESCAEQFPIL  1500
1501  DTSVQFWYEFIDYIMRVIEEDQKNYTPALNQFPQELNVGNLSAETLWSMY  1550
1551  KNDLKMALEEHAQKKRCKTPEYMNLYFKVKGFYFKYVADLSTYKSSIPEF  1600
1601  PAWFIPFVMDWLNENDEHSMDILRNAYNVDKADNFPQTSEHTKFSNSVVD  1650
1651  VFTQLNAALKLLKQMDCPNPEVAADMMKRFSKTLNKVLLAYADMVQKDFP  1700
1701  KFAHDEKLACILMNNVQQLRVQLEKIYETMGGAELDEHIGQVLTVLQKKL  1750
1751  NSVLDRLSAEFVTTLEPHIHEQTIKLGMLLVKIKGPQLQKTQVQPEADAV  1800
1801  LEPLMDLLEGSLRRYADQCEKTVLKYILKELWKITIVNMEKRVVLPPLSD  1850
1851  KALLKQLPNAKIGDVTKLMSTNIQSIKGMNSVKDMMDMARESEKSLTPRQ  1900
1901  CTVLDCALDAIKDSFHASGKGLKKSFFEKSPELQSLKYALSLYTQTTEQL  1950
1951  IKTFITSQRQQDLPSQEQPVGEVSVQVDLFSHPGTGEQKVTVKILAANDL  2000
2001  RWQTSSAFKPFVEVHLVGPHLSDKKRKWSTKTKAGNWAPKFNETFHFFLG  2050
2051  NEGEPEHYELMFQVKDYCFARDDRVVGVGVLQLSSVVDQAGSCAMWVQLG  2100
2101  TRLHIDETGLILLRILSQRQTDEVAKDFVRLKTECRYETETVMAASASSQ  2150
2151  NINRT                                               2155

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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