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

NucPred

Fetching P51826 from www.uniprot.org...

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

   1  MDSFDLALLQEWDLESLCVYEPDRNALRRKERERRNQETQQDDGTFNSSY    50
51 SLFSEPYKTNKGDELSNRIQNTLGNYDEMKDFLTDRSNQSHLVGVPKPGV 100
101 PQTPVNKIDEHFVADSRAQNQPSSICSTTTSTPAAVPVQQSKRGTMGWQK 150
151 AGHPPSDGQQRATQQGSLRTLLGDGVGRQQPRAKQVCNVEVGLQTQERPP 200
201 AMAAKHSSSGHCVQNFPPSLASKPSLVQQKPTAYVRPMDGQDQAPDESPK 250
251 LKSSSETSVHCTSYRGVPASKPEPARAKAKLSKFSIPKQGEESRSGETNS 300
301 CVEEIIREMTWLPPLSAIQAPGKVEPTKFPFPNKDSQLVSSGHNNPKKGD 350
351 AEPESPDNGTSNTSMLEDDLKLSSDEEENEQQAAQRTALRALSDSAVVQQ 400
401 PNCRTSVPSSKGSSSSSSSGSSSSSSDSESSSGSDSETESSSSESEGSKP 450
451 PHFSSPEAEPASSNKWQLDKWLNKVNPHKPPILIQNESHGSESNQYYNPV 500
501 KEDVQDCGKVPDVCQPSLREKEIKSTCKEEQRPRTANKAPGSKGVKQKSP 550
551 PAAVAVAVSAAAPPPAVPCAPAENAPAPARRSAGKKPTRRTERTSAGDGA 600
601 NCHRPEEPAAADALGTSVVVPPEPTKTRPCGNNRASHRKELRSSVTCEKR 650
651 RTRGLSRIVPKSKEFIETESSSSSSSSDSDLESEQEEYPLSKAQTVAASA 700
701 SSGNDQRLKEAAANGGSGPRAPVGSINARTTSDIAKELEEQFYTLVPFGR 750
751 NELLSPLKDSDEIRSLWVKIDLTLLSRIPEHLPQEPGVLSAPATKDSESA 800
801 PPSHTSDTPAEKALPKSKRKRKCDNEDDYREIKKSQGEKDSSSRLATSTS 850
851 NTLSANHCNMNINSVAIPINKNEKMLRSPISPLSDASKHKYTSEDLTSSS 900
901 RPNGNSLFTSASSSKKPKADSQLQPHGGDLTKAAHNNSENIPLHKSRPQT 950
951 KPWSPGSNGHRDCKRQKLVFDDMPRSADYFMQEAKRMKHKADAMVEKFGK 1000
1001 ALNYAEAALSFIECGNAMEQGPMESKSPYTMYSETVELIRYAMRLKTHSG 1050
1051 PNATPEDKQLAALCYRCLALLYWRMFRLKRDHAVKYSKALIDYFKNSSKA 1100
1101 AQAPSPWGASGKSTGTPSPMSPNPSPASSVGSQGSLSNASALSPSTIVSI 1150
1151 PQRIHQMAANHVSITNSILHSYDYWEMADNLAKENREFFNDLDLLMGPVT 1200
1201 LHSSMEHLVQYSQQGLHWLRNSAHLS 1226

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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