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

NucPred

Fetching Q9UQ26 from www.uniprot.org...

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

   1  MSAPVGPRGRLAPIPAASQPPLQPEMPDLSHLTEEERKIILAVMDRQKKK    50
51 VKEEHKPQLTQWFPFSGITELVNNVLQPQQKQQNEKEPQTKLHQQFEMYK 100
101 EQVKKMGEESQQQQEQKGDAPTCGICHKTKFADGCGHNCSYCQTKFCARC 150
151 GGRVSLRSNKVMWVCNLCRKQQEILTKSGAWFYNSGSNTPQQPDQKVLRG 200
201 LRNEEAPQEKKPKLHEQTQFQGPSGDLSVPAVEKSRSHGLTRQHSIKNGS 250
251 GVKHHIASDIASDRKRSPSVSRDQNRRYDQREEREEYSQYATSDTAMPRS 300
301 PSDYADRRSQHEPQFYEDSDHLSYRDSNRRSHRHSKEYIVDDEDVESRDE 350
351 YERQRREEEYQSRYRSDPNLARYPVKPQPYEEQMRIHAEVSRARHERRHS 400
401 DVSLANADLEDSRISMLRMDRPSRQRSISERRAAMENQRSYSMERTREAQ 450
451 GPSSYAQRTTNHSPPTPRRSPLPIDRPDLRRTDSLRKQHHLDPSSAVRKT 500
501 KREKMETMLRNDSLSSDQSESVRPPPPKPHKSKKGGKMRQISLSSSEEEL 550
551 ASTPEYTSCDDVEIESESVSEKGDSQKGKRKTSEQAVLSDSNTRSERQKE 600
601 MMYFGGHSLEEDLEWSEPQIKDSGVDTCSSTTLNEEHSHSDKHPVTWQPS 650
651 KDGDRLIGRILLNKRLKDGSVPRDSGAMLGLKVVGGKMTESGRLCAFITK 700
701 VKKGSLADTVGHLRPGDEVLEWNGRLLQGATFEEVYNIILESKPEPQVEL 750
751 VVSRPIGDIPRIPDSTHAQLESSSSSFESQKMDRPSISVTSPMSPGMLRD 800
801 VPQFLSGQLSIKLWFDKVGHQLIVTILGAKDLPSREDGRPRNPYVKIYFL 850
851 PDRSDKNKRRTKTVKKTLEPKWNQTFIYSPVHRREFRERMLEITLWDQAR 900
901 VREEESEFLGEILIELETALLDDEPHWYKLQTHDVSSLPLPHPSPYMPRR 950
951 QLHGESPTRRLQRSKRISDSEVSDYDCDDGIGVVSDYRHDGRDLQSSTLS 1000
1001 VPEQVMSSNHCSPSGSPHRVDVIGRTRSWSPSVPPPQSRNVEQGLRGTRT 1050
1051 MTGHYNTISRMDRHRVMDDHYSPDRDRDCEAADRQPYHRSRSTEQRPLLE 1100
1101 RTTTRSRSTERPDTNLMRSMPSLMTGRSAPPSPALSRSHPRTGSVQTSPS 1150
1151 STPVAGRRGRQLPQLPPKGTLDRKAGGKKLRSTVQRSTETGLAVEMRNWM 1200
1201 TRQASRESTDGSMNSYSSEGNLIFPGVRLASDSQFSDFLDGLGPAQLVGR 1250
1251 QTLATPAMGDIQVGMMDKKGQLEVEIIRARGLVVKPGSKTLPAPYVKVYL 1300
1301 LDNGVCIAKKKTKVARKTLEPLYQQLLSFEESPQGKVLQIIVWGDYGRMD 1350
1351 HKSFMGVAQILLDELELSNMVIGWFKLFPPSSLVDPTLAPLTRRASQSSL 1400
1401 ESSTGPSYSRS 1411

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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