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Similarity between protein sequences is usually predictive of similarity in structures. However, in some rare cases protein domains with significant sequence similarity adopt different structures. Here, we carry out a survey of protein domain pairs with high sequence similarity (measured by HHsearch probability) and low structural similarity (measured by Dali Z-score), aiming to identify the reasons for this discordance. Besides methodological problems with either sequences or structures of domains, we find and describe novel examples of homologs with structural changes.