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

NucPred

Fetching Q8GU86 from www.uniprot.org...

The NucPred score for your sequence is 0.41 (see score help below)

   1  MAGEITPSGSRRSWLSSGAASLARSLRDGDDPFRRSAAASRRDAGDDEEN    50
  51  LRWAALEKLPTYDRMRRGILRKAVDGGGDGEGAGSLFKADEVDIANLDPR   100
 101  EGRELMERVFKAVEDDNERFLRRFRDRLDQVGIELPKIEVRYQHLDIEAD   150
 151  VHVGKRALPTLLNATINTLEGLVSLFISSNKRKLKILNDVNGIIKPSRMT   200
 201  LLLGPPSSGKSTLMRALTGKPDKNLKVSGEITYCGHTFKEFYPERTSAYV   250
 251  SQHDLHNPEMTVRETLDFSRRCLGSGARYDMLSELTRRERNAGIKPDPEI   300
 301  DALMKATVVEGKQNNIVTDLVLKALGLDICADTIVGGAMIRGISGGQKKR   350
 351  VTTGEMLTGPATALFMDEISTGLDSSSTFQIVKYIRQVTHVMNATVMMSL   400
 401  LQPPPETYALFDDIVLIAEGYIVYHGPRENILEFFESAGFRCPERKGVAD   450
 451  FLQEVTSRKDQQQYWFLEQDHYRYVSVEEFAQNFKKFHVGQKLQKELQVP   500
 501  YDKSKTHPAALTTKKYGLSSLESLKAVMSREWLLMKRNSFLFIFKAFQLF   550
 551  VLGFITMTLFLRTKMPHEKFSDTSKYVGALTASLITIMFNGFGELQLTID   600
 601  KLPIFYKQRDFLFFPAWTYGLANIILKVPLSLMESSLWIVLTYYVVGFAP   650
 651  AAGRFFKQFLAYFWTHQMALALFRLLGAILRSMVVANTFGMFVLLLIFLF   700
 701  GGFLVSRKDIKPWWIWGYWTSPMMYSNNALSVNEFLASRWAIPNNDSSIS   750
 751  APTIGKAFLQSKGYFTGEWGYWLSIGAMIGFMIVFNILYLCALTFLRPIG   800
 801  SASTVVSDDDTKSELEAESNQEQMSEVINGTNGTENRRSQRGMVLPFQPL   850
 851  SLSFNHMNYYVDMPAEMKAQGFTESRLQLLSDISGAFRPGVLTALVGVSG   900
 901  AGKTTLMDVLAGRKTSGTIEGDIKLSGYPKKQETFARISGYCEQTDIHSP   950
 951  NLTVYESIVYSAWLRLSSEVDKNTRKVFVEEVMSLVELDVLRDALVGLPG  1000
1001  VSGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTV  1050
1051  NTGRTVVCTIHQPSIDIFESFDELLLLKRGGRVIYAGQLGLHSQILVEYF  1100
1101  EAIPGVPKITEGYNPATWMLEVSSSLAEARLDIDFAEVYANSALYRSNQE  1150
1151  LIKQLSVPPPGFQDLSFPTKYSQNFLNQCVANTWKQFQSYWKDPPYNAMR  1200
1201  YVMTLLYGLVFGTVFWRRGKNIESVNDLNNLLGATYAAVFFLGAANLLTL  1250
1251  LPVVSVERTVFYREKAAGMYSPLSYAFAQGFVEFCYSAVQGVLYTILIYS  1300
1301  MIGYEWKADKFFYFLFFMIAAFAYFTLFSMMLVACTASEMLAAVLVSFVL  1350
1351  SSWNNFAGFIIPRPLIPVWWRWFYWANPVSWTIYGVIASQFADSDRVVTV  1400
1401  PGQSTTMVVKDFLEKNMGFKHDFLGYVVLAHFGYVIIFFFLFGYGIKCLN  1450
1451  FQKR                                                1454

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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