mRNAs were also enriched for binding (heme binding, tetrapyrrole binding, iron ion binding, cation binding and metal ion binding), which is common in the Arabidopsis root [ 30].
A search of AtcisDB for these motifs returned 4 showing a partial match to the record of 'PRHA binding sites' (Table 1), which is derived from the report of Plesch et al. [ 27], describing auxin-induced expression of the Arabidopsis prha homeobox gene.
We identified three novel AR matrices (Figure 4) that can be mapped to 1,448, 1,012, 317 AR binding regions respectively (Table S6 S7), which is much higher than the number of mapped AR binding regions using the three known canonical AR motifs from the Transfac database as we showed above.
For instance, CBS is able to identify within a group of co-regulated genes reported to be relevant for wing imaginal disc regeneration a significant enrichment on AP1 binding sites (see Table 2), which is a downstream target of the JNK signaling pathway that is precisely activated in wound healing stages [ 51].
Superposition (overlapping of Cα atoms) of modeled AGPase SS with their structural homologue in DS3.5 reveals that the spatial position and orientation of substrate and inhibitor binding site are highly conserved and 4(b) and Figures 5(a) and 5(b)) and shows a very low RMSD within the substrate and inhibitor binding site which is evident from Table 7.
The binding information, which is shown in a table in Fig. 2, is managed in the hierarchy DNS-RVS-proxy to enable reachability of an MH which is registered with the mobility-enabled HIP proxy.
In addition, FNLDH shows significant positive homotropic cooperativity also for NADH binding, which is less affected by FBP or Mg2+ than pyruvate binding (Table 3), suggesting that FNLDH changes in its structure through two steps, the NADH binding and following pyruvate binding steps, in the allosteric transition.
Consistent with this model, we observed a 10-fold elevation in SKO mice of the direct PPARδtarget heparin-binding EGF-like growth factor (Hbegf; Table 7), which is elevated in psoriasis and induces epidermal hyperplasia [56].
The putative soybean MMP gene Glyma02g03301 has two cysteine switch motifs and two zinc-binding motifs, which is indicated in the table.
There are also many putative transcription factors and DNA binding proteins (Table 2), which are good candidates for regulators of ovule development.
