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

NucPred

Fetching Q767L8 from www.uniprot.org...

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

   1  MEDTQVINWEAEEEEVEEGPSEPLGCNLQPVGQLRIFSSSYGPEKDFPLY    50
  51  LGKNVVGRMPECSVALPFSSISKQHAVIEILAWNKAPVLRDCGSLNGTQI   100
 101  LRPPKVLGPGVSHRLRNRELILFADLPCQYHRLDVPPPLVSRGPLTVEET   150
 151  PRGQGGTQPHRLLLAEDSEEEVDSLSERCVVKGPKTSLTTVIPESDEEGP   200
 201  SPAPDGPGPPFAFNLNSDTDEEESQQPGAGEAPSAAETEQPKPVTTEIQL   250
 251  IKDQCPVKEKHKDARVKRAASNGVVPVGAILERSQPAGEDSDTDVDEGSG   300
 301  LPRRPAGAHSERAQPCGFIDSDTDAEEEGIPATPAVVPVKKRQIFHEVGT   350
 351  ESPQAPGVAHAQESPAGSDTDIEEGEAPRTVPLDSSRASMMIDSNMDDEE   400
 401  EVSAALTLARLRESQAVPWNRDAGAGDHRAQPVALLDQSQASAGRDSDTD   450
 451  MEEEGLPLEKRGSLPKGPADKAHPEKSQPPLRGSDVKVEEDERSPGVHPG   500
 501  RSQASATVDAITQVEEKAPPRPAVTLSEQHQVPVAWTPQTDVEAEGDPAK   550
 551  LPVVHPAEARPPPAGGHEPDVEKNTSLAASAGADVRKSQLLAEGDAGTEW   600
 601  AVAILAQDRALGAGAQSVSARAQVGQDLPLVSREHLADVAVDTGAPGEAT   650
 651  QTQREGTQALTERERELNVDRTIDSGDNRDDSEDLDLQATQCFVEGENQS   700
 701  PEAVPSMEDEPTQAFPSTLPQEPGPSCCSFQASGTLDEPWELLATQPFCP   750
 751  RESEASEIQPVDTHLEARGLCPSPPRAALPEQHPESPEPLGSQGGGRQTV   800
 801  EKATGTPRETAEGPTPERGPLERATKEPPSEGERGGMGEEGLPRGTQDRE   850
 851  EKQVLAGVTQRQESDRTVKSTSTDGGLESLQVEIETPKEMQENEIEKQTL   900
 901  ARDMLEREAEKPVAERESEAGGPEVKVPEAVQDRGPLRAEAEGTSQDQKG   950
 951  QASNLTPEPGAGVGYLQGLASAPAAPRSQAGGGGEAPVSPRRQQRGDLNC  1000
1001  KMPPAEKSGVRAAFSPSLPSPHGDQESPEACLPPEPPEASAPLQNPLPSQ  1050
1051  SPKHPAPQSRLSPPPPPLEQSTPRTRPPQSQESPEPPFSSELDPPNPEPK  1100
1101  VRPQGSPPLSPIPLEAHPTSPTDQAGSPEPTSRAARGGTHRSFEVTPMSV  1150
1151  VPTALELQSSTSADQPVVPKPTLRAPWGRTHRSSVKTPEPNIPTAPELQP  1200
1201  STPTDQPVAPEPLSRATRGRTPRASVKTSEPVVPAAPEPQPSTPTDQPVV  1250
1251  PKPTLRAPRGRTHRSSVKTPEPNIPTAPELRPSTPTDQPVAPEPLSRATR  1300
1301  GRTPRASVKSPEQNVPTAPEHPQPSTPTDQPVTPKPTSRATRGRAHRSSV  1350
1351  KTPAASEPLPSASTDQPITPKPTSRGRAHRSSAKTPELQPPTSTGQPVTP  1400
1401  RPTSQATRGRTHRSSIKTPEPVVPTDPEPQPSTPTDQPITPELTSAATRG  1450
1451  RTRRSSVKTPEPVVPTDPEPQPSTPTDQPITPKPTSWATRGQAHRSSVKT  1500
1501  PEPHVPTDPEPQPSTPTDQPVTPKPTSRATRGRARKSSVKTPEPAVPTAA  1550
1551  EPQPSASTDQPITPKPTSRGRAHRSSAKTPELQPPTSTGQPFTPRPTSGA  1600
1601  TQGRTHRSSAKTSQAVEPTAPDLEPPSPIGQPVTPKVIAEGGQNRILRSS  1650
1651  RVGAVPGPTPPELQCPVPTEQPVPPEPIPRASCSRRPRATRKRESLTAHV  1700
1701  GPDPCSAPPEPNSRSSRTQSLSTTPEPTLPQLPEAPAHAPQIPKVEAAGR  1750
1751  PGFTLEPQPKATQKRKRPLAPADSPPLPKRLQRGEVPPKTVILEEEENPT  1800
1801  ARPGREEDAVIPEPGKRKRDQTEEEPRGVPSRSLRRTKPAQESTAPRVLF  1850
1851  TGVVDARGERAVLALGGSLASSVAEASHLVTDRIRRTVKFLCALGRGIPI  1900
1901  LSLDWLHQSRKAGCFLPPDEYVVTDPEQEKNFGFSLREALSRARERKLLE  1950
1951  GYEIHVTPGVQPPPPQMGEIISCCGGTVLPSMPRSYKPQRVVITCSQDFP  2000
2001  RCSVPFRLGLPVLSPEFLLTGVLKQEAKPEAFVLSTLEMASA          2042

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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