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Evolutive history of Hyc and Hyf proteins from Caldanaerobacter subterraneus subspecies.

Apparently, these hyc and hyf genes shared common evolutionary histories and were acquired together as a cluster, not individually (Fig.  3 and Additional file 2: Table S1).

Additionally, we have shown detailed examples of two highly conserved orthoblocks (atp and ydc) and two less-conserved orthoblocks (paa and hyf).

In fact, the hyc and hyf genes of Thermoanaerobacter sp. YS13 have identity values higher than 96%% at the nucleotide level when compared to the C. subterraneus subsp. tengcongensis orthologous genes.

The hyc and hyf operons encode for paralogous energy-converting Ni-Fe hydrogenases Hyd-3 and Hyd-4 of E. coli, which have significant similarity to the components of NADH quinone oxidoreductase (complex I), suggesting their implication in energy metabolism [ 23].

E. coli possesses four hydrogenases; two of which, Hyd1 (hya) and Hyd2 (hyb), normally function in hydrogen oxidation, and two others, Hyd3 (hyc) and Hyd4 (hyf), which function physiologically in proton reduction.

However, because of the lack of at least four subunit-encoding genes, and the structural differences in the CH34 and H16 Hyf proteins compared to the E. coli K12 Hyf units, it is very unlikely that the hyf genes in either strain are involved in any aspect of lithotrophic growth.

HXZ, GZN, HYF and WDR collected the patient data and involved in the interpretation of data.

Interestingly, both E. coli FHL complexes are encoded by two operons, Hyf and Hyc [ 41].

In E. coli, the FHL type hydrogenase groups with genes of the hydrogenase 3 and hydrogenase 4 (hyf) systems.

The pharmacophore model of PXR is displayed in Figure 2. Remarkably, besides three different conformations of SRL12813, other agonists of PXR in the Protein Data Bank (PDB) were predicted exactly by our pharmacophore model such as RFP, HYF, PNU, and T0901317.