## 3 Results and Discussion
### BLUF Modules in Association with the Effector Domains
#### 3.3.7 DNA pol 3 gamma3 Superfamily  
In _E. coli_, DNA polymerase III (Pol III) is a complex holoenzyme comprised of three functionally distinct subassemblies, i.e., the core polymerase (\(\alpha\), \(\varepsilon\), and \(\theta\) subunit), the sliding clamp (\(\beta\) subunit) and the clamp loader complex (\(\tau\)2\(\gamma\)\(\delta\)\(\delta\)\(\chi\)\(\psi\) subunit) [108]. The clamp loader is responsible for the DNA-dependent hydrolysis of ATP to load \(\beta\)2 clamps onto DNA for the interaction with core polymerases [109]. The gene _dnaX_ encodes the ATP motor subunits of the clamp loader, i.e., one \(\gamma\) and two \(\tau\) subunits, where the \(\gamma\) subunits are considered as a truncated product of the \(\tau\) subunits [110; 111]. The gamma (\(\gamma\)) subunit shares domains I-III with the tau (\(\tau\)) subunit, while the domain IV and the entire alpha-interacting domain V subunit are only observed in the \(\tau\)-subunit. The bacterial DNA pol III \(\gamma\) III domain and its homolog, the eukaryotic replication factor C (RFC), belong to the AAA-ATPase superfamily and are primarily involved in the breaking or restructuring of the supramolecular assembly of proteins [110]. In this communication, we have selected two BLUF modular domains in association with the DNA pol III \(\gamma\) III domain only (accession number AIQ92835.1) from _Methylobacterium oryzae_ CBMB20, and the PRK11633-DNA pol III \(\gamma\) III domain (WP_048452447.1) from _Methylobacterium_ _tarhaniae_ (Table 1).  
Furthermore, we have performed the alignment of the sequences representing the DNA pol III \(\gamma\) III domain against the well-characterized truncated sequence (1-373 amino acids) of the DNA polymerase III subunit gamma/tau (WP_113440333.1) from _E. coli_ (Figure S5). The sequences corresponding to the DNA pol III \(\gamma\) III domains aligned against the domain II of the \(\gamma\) III subunit of DNA pol III from _E. coli_; however, most of the critical amino acids are not conserved amongst the DNA pol III \(\gamma\) III domain. In the _E. coli_ DNA pol III \(\gamma\) III domain, Thr157, responsible for the hydrogen bond formation with the terminal phosphate of AMP-PNP, is only conserved in the DNA pol III \(\gamma\) III domain from _Methylobacterium tarhaniae_ but not in _Methylobacterium oryzae_ CBMB20 (Figure S5) [110]. Moreover, the C-terminal SARC motif (Ser168, Arg169, and Cys170) located in the \(\alpha\)\(\gamma\) helix in the sensor1 region, which is highly conserved in the \(\gamma\) subunit of almost all organisms [112; 113], is found missing in both of the DNA pol III \(\gamma\) III domains. Arg169 has dual roles, where on the one hand it acts as an \"arginine finger\" for the SARC motif, while on the other hand it is responsible for electrostatic and hydrophobic interactions which hold the \(\delta\) subunit onto the \(\gamma\) III subunit. Arg215 is another critical amino acid and is a part of the conserved motif G/P\(\chi\)\(\Phi\)RX\(\Phi\) (where \(\Phi\) is any hydrophobic residue) located in the DNA pol III \(\gamma\) III domains, among prokaryotes as well as among eukaryotes [112]. The correct alignment of Arg215 is very crucial for its proper interaction with the phosphate group of ADP/ATP [110]. From the multiple sequence alignment analysis, it was observed that this particular amino acid is conserved in the BLUF-DNA pol III \(\gamma\) III domains but replaced by another polar amino acid (tyrosine:Q) in the BLUF- PRK11633-DNA pol III \(\gamma\) III domain (Figure S5).  
The protein-protein interaction analysis revealed that most of the interacting partners of DNA pol III \(\gamma\) III (dnaX) are the components involved in the regulation of DNA replication, such as DNA pol I (Pol A), replicative DNA helicase (dnaB), DNA mismatch repair protein (recR), DNA pol III subunit \(\alpha\) (dnaE), \(\delta\) (holA and holB), \(\varepsilon\) (dnaQ), chi (holC), psi (holD) and \(\beta\) sliding clamp (dnaN) (Figure S7e and Table S1).