hfAIM: high fidelity autophagy-associated atg8-interacting motifs detecting tool
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hfAIM: a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated atg8-interacting motifs in various organisms

Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements – the presence of acidic amino acids and the absence of positively charged amino acids in certain positions - to reliably identify AIMs in proteins.

For calculating a position specific scoring matrix (PSSM), we recommend using the iLIR tool.
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Atg8-interacting proteins often possess one or more functional Atg8-interacting motifs (AIMs), which are comprised by the core consensus sequence F/W/Y-X-X-L/I/V.1, 3, 5
The presence of acidic amino acids either immediately upstream the F/W/Y sequence or at any of the two X positions in between the F/W/Y and the L/I/V sequences appear to contribute to the fidelity of binding of Atg8 to the AIM.

Thus, it might be useful to consider a longer six amino acid X-2-X-1-F/W/Y-X+1-X+2-L/I/V motif for AIMs. Based on this degenerate sequence, the five regular expression motifs below (selected by default) are recommended to be screened in your protein sequences of interest. Drag or hold CTRL to select multiple patterns

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  5. XX[DE][WFY][DE]X[LIV]
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To cite this article: Qingjun Xie, Oren Tzfadia, Matan Levy, Efrat Weithorn, Hadas Peled-Zehavi, Thomas Van Parys, Yves Van de Peer & Gad Galili (2016): hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms, Autophagy, 12(5):876-87 DOI: 10.1080/15548627.2016.1147668