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

NucPred

Fetching Q5DU25 from www.uniprot.org...

The NucPred score for your sequence is 0.86 (see score help below)

   1  MEAGSGPPGGPGSESPNRAVEYLLELNNIIESQQQLLETQRRRIEELEGQ    50
  51  LDQLTQENRDLREESQLHRGELHRDPLGARDSPGRESQYQNLRETQFHHR   100
 101  ELRESQFHQASRDVGYPNRDGAYQNREAIYRDKEREASYQLQDTTGYTAR   150
 151  ERDVAQCHLHHENPALGRERGGREAGPAHPGREKEAGYSAAVGVGQRPPR   200
 201  ERGQLSRGASRSSSPGAGGGHSTSTSTSPATTLQRNVEGDAPGSDLSTAV   250
 251  DSPGSQPPYRLSQLPPTSSHMGGPPAGVGLPWAQRARLQPASVALRKQEE   300
 301  EEIKRSKALSDSYELSTDLQDKKVEMLERKYGGSFLSRRAARTIQTAFRQ   350
 351  YRMNKNFERLRSSASESRMSRRIILSNMRMQFSFEEYEKAQNPAYFEGKP   400
 401  ASLDEGAMAGARSHRLERGLPYGGSCGGGIDGGGSSVTTSGEFSNDITEL   450
 451  EDSFSKQVKSLAESIDEALNCHPSGPMSEEPGSAQLEKRESKEQQEDSSA   500
 501  TSFSDLPLYLDDPVPPPSPERLPSTEPPPQGRPEFWAPAPLPPVPPPMPP   550
 551  GTREDGSREEGTRRGPGCLECRDFRLRAAHLPLLTIEPPSDSSVDLSDRS   600
 601  DRGSVHRQLVYEADGCSPHGTLKHKGPPGRAPIPHRHYPAPEGPAPAPPG   650
 651  PLPPAPNSGTGPSGVAGGRRLGKCEAAGENSDGGDNESLESSSNSNETIN   700
 701  CSSGSSSRDSLREPPATGLCKQTYQRETRHSWDSPAFNNDVVQRRHYRIG   750
 751  LNLFNKKPEKGIQYLIERGFLSDTPVGVAHFILERKGLSRQMIGEFLGNR   800
 801  QKQFNRDVLDCVVDEMDFSSMDLDDALRKFQSHIRVQGEAQKVERLIEAF   850
 851  SQRYCVCNPALVRQFRNPDTIFILAFAIILLNTDMYSPSVKAERKMKLDD   900
 901  FIKNLRGVDNGEDIPRDLLVGIYQRIQGRELRTNDDHVSQVQAVERMIVG   950
 951  KKPVLSLPHRRLVCCCQLYEVPDPNRPQRLGLHQREVFLFNDLLVVTKIF  1000
1001  QKKKILVTYSFRQSFPLVEMHMQLFQNSYYQFGIKLLSAVPGGERKVLII  1050
1051  FNAPSLQDRLRFTSDLRESIAEVQEMEKYRVESELEKQKGMMRPNASQPG  1100
1101  GAKDSVNGTLARSSLEDTYGAGDGLKRGALSSSLRDLSDAGKRGRRNSVG  1150
1151  SLDSTIEGSVISSPRPHQRMPPPPPPPPPEEYKSQRPVSNSSSFLGSLFG  1200
1201  SKRGKGPFQMPPPPTGQASASSSSASSTHHHHHHHHHGHSHGGLGVLPDG  1250
1251  QSKLQALHAQYCQGPGPAPPPYLPPQQPPLPPPPQQPPPLPQLGSIPPPP  1300
1301  ASAPPVGPHRHFHAHGPVPGPQHYTLGRPGRAPRRGAGGHPQFAPHGRHP  1350
1351  LHQPTSPLPLYSPAPQHPPAHKQGPKHFIFSHHPQMMPAAGAAGGPGSRP  1400
1401  PGGSYSHPHHPQSPLSPHSPIPPHPSYPPLPPPSPHTPHSPLPPTSPHGP  1450
1451  LHASGPPGTANPPSANPKAKPSRISTVV                        1478

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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