Fig. 1. Comparison of Hox cluster organization and sequence between C. elegans and Drosophila. (A) Drosophila contains eight Hox genes, organized into two subclusters. In C. elegans, the four core members are in one cluster, interspersed by many other unrelated genes. Two additional Hox genes, php-3 and nob-1, are located elsewhere in the genome. ceh-13, the labial ortholog of C. elegans, is not in a distal position in the cluster as it is in other organisms. (B) Hox gene organization and sequence identity (for the different parts of the proteins) of orthologous and paralogous genes at the amino acid level. Hox genes can be subdivided into the N-terminal and the C-terminal parts. Both, hexapeptide (hp) and homeodomain are localized in the C-terminal part of the protein. Within the homeodomain itself, the N-terminal arm (Na) and helices I, II and III (HI, HII, HIII) can be distinguished. The C-terminal end refers to the protein-coding part between the end of the homeodomain and the end of the protein. The numbers to the left indicate percentage of overall sequence similarity; the three following numbers refer to the sequence similarity in the N-terminal part (second number), the hexapeptide and homeodomain region (third number) and the C-terminal end (last number), respectively. (C) Amino acid sequence comparison of the Hox proteins shown in B in the homeodomain region. Black, sequence identity; gray, sequence similarity. (D) Amino acid sequence comparison of Cel-mab-5 and Ppa-mab-5 over the complete protein.

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