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

NucPred

Fetching Q25197 from www.uniprot.org...

The NucPred score for your sequence is 0.66 (see score help below)

   1  MMRNVQSFYFLFLLIVLNFHVVLSAVCIGQRATTTIWLNQNGDCQDVGFC    50
  51  QYLQNCTCWHGNLVVKSTKYYDEENFKPYFPKLREITGYLLISLCTLKFF   100
 101  HLFPGLTVIRGGDLILNYALVIYYNEIKEVYFPSLTAILNGGVHIGRNHR   150
 151  LCYVNTIRWKSIIKDIHQTGQYGIYLESNKLNCDLGCLKGHCHPAPGHDG   200
 201  DPKAQYCWGPGPKKQQNKAQCQRFCNTQCGPEGCLDGSDHICCHHECLGG   250
 251  CSAINSTNTCHACRKYRIKSTGQCVSKCPRKQYLVDKFLCQESCPYWSIN   300
 301  STEYHHYLWQGECVTKCPVNYISNNQTKKCEKCKSGMKCNTVCKYQDVMA   350
 351  DGTLYNGALIRVPSDISKKGLVGCSVFEGSLTFQLQEGTGKAEDSLNELK   400
 401  SLKVLKGHLKIQKSSLKSLNFLSSLEVIETPQNALLHNKYVMAVYENSQL   450
 451  SELWPGNESIIVSDGGIFFQYNPRLCPLHIRNLQDRIHYKNGSKVTGEVS   500
 501  LQNNGHKVLCDTQMLVMHVEEFIPPDLNMETDMTAIECNSFKCVKVTWNF   550
 551  TMTSAYNNILFYAIYFKELQSNQEAVVQLDNECQNNDDWNVITVDIPKIE   600
 601  SLEQSLFLQSKIISKLTPYTRYAFYIKEIVSKGEERSSHIHYINISQDLP   650
 651  SEPLGVEASFLSENKILLKWRAPSKPNGIITAFKIYYNKPDYSFWEEQKV   700
 701  LDWCSRDASRDKNAKDVAGYPVNKENYNQYCNISCVCDEEKENSKAIKAD   750
 751  REAHNFNVEFQTELMRVLFTKNKFSYRNKNKSPPKIDFSKNISLILSNKI   800
 801  LTSTSTTVTQAKIEIIEEPKVTVNGNIFSYVISGLDYFEDYELKVCGCTV   850
 851  VGCRRPSSTINLDCGIVQARTGVNLTADNLDSKMVRVQVQLDSYNISWIA   900
 901  PHKPNAVILKYEISIRYALDKDALVICRPGYLPTYIIRKSRFGNYVAKIR   950
 951  AISPAGNGSWTEEIHFKVAELSVTKNNNQLIIGIISAVSAVIVALLVFIL  1000
1001  LYMFLHRKLEKDVQGVLYASVNPEYMNSKEVYIPDEWELNREKIELIREL  1050
1051  GQGSFGMVFEGIAHGIGDHAELRVAVKTTNENASIHDRIQILQEASIMKA  1100
1101  FNCNHVVKLIGVVSQGQPTFVVMELMGRGDLKSYLKERRPDDGGIPLMRQ  1150
1151  EIYQMVAEIADGMAYLAARKFVHCDLAARNCMVASDFTVKIGDFGMARDI  1200
1201  YERNYYRKDGKSLLPIRWMAPESLKDGIFSTASDVWSFGVVLWEICTLAS  1250
1251  QPYQGKTNEQVLNFVLSNGHLDYPEGCDYQLREFMSLCWHRDPKMRPSFL  1300
1301  EIVHVLENEVDDDFVMVSFYHEMKRKALEDIYMKSESYIKSDAYTMSDGY  1350
1351  TKGDGNMQNMLSRSQNRKSAIEKSKERLSISSLDSGTYVEKYDANDTPEE  1400
1401  IPKKKKRPRSKRNSAVDSNACETKPMLRVESLYDNHDAFSENMQYGDTPV  1450
1451  GKSDLMHPETNRELRLSEIFYGKPIPV                         1477

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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