# RECTA: Region Identification Based on Comparative Genomics and Transcriptomics Analysis
## 3 Results
### Verified Regulons Based on Literature Verification  
Altogether, 36 literature-supported ASR-related transporters were successfully mapped to MG1363 using blast with an E-value cutoff as 1e\({}^{-10}\), which resulted in a total of 33 mapped genes. All the 36 transporters were categorized into nine modules based on their biological functions or regulated pathways, including L-lactate dehydrogenase (LDH), GAD, ADI, urea degradation, F1/FOATPase, acid stress, protein repair and protease, envelope alterations, and DNA repair. The 33 mapped genes generate 22 operons and six regulons: _llrA_, _llrC_, _hllA_, NHP6A, regulon #8 and #39, which were subjected, one or more, to each functional module (Table 2). \begin{table}
\begin{tabular}{l l l l l} \hline \hline
**Template Organisms** & \multicolumn{3}{c}{**MG1363**} \\ \hline
**Organisms** & **Transporters** & **Functions/Pathways** & **Mapped Genes (Locus Tag)** & **Regulons** \\ \hline \multirow{3}{*}{_Lactococcus lactis_} & _llth_ & & _llth_ (llmg\_1120) & NHP6A, \\  & _llthB_ & LDH & _llthB_ (llmg\_0392, llmg\_0475) & _llrA_ \\  & _llthX_ & & _llthX_ (llmg\_1429) & \\ \hline \multirow{3}{*}{_Lactococcus lactis_} & _galB_ & & _galC_ & _galB_ (llmg\_1179) & \\  & _galC_ & & _galC_ (llmg\_1178) & N/A \\ \hline \multirow{3}{*}{_L actococcus lactis_} & _arcA_ & & _arcA_ (llmg\_2313) & \\  & _arcB_ & & _arcB_ (llmg\_2312) & \\  & _arcC1_ & ADI pathway & _arcC_ (llmg\_2310) & NHP6A, \\  & _arcC2_ & & _arcC_2 (llmg\_2309) & _llrA_, _llrC_, _llIA_ \\  & _argF_ & & _argF_ (llmg\_1754) & \\ \hline Bacteria & _arcA_/B/C\$ & & Urea degradation & _pyrC_ (llmg\_1508) & N/A \\ \hline \multirow{3}{*}{_L actococcus lactis_} & _atpEBFHAGDC_$ & & & llmg\_1952, lmg\_1951, \\  & & & & llmg\_1950, lmg\_1949, \\  & & & & llmg\_1948, lmg\_1947, \\  & & & & llmg\_1946, lmg\_1945 \\ \hline \multirow{3}{*}{_Lactococcus lactis_} & _rrfB_ & Acid response & _rcfB_ (llmg\_2512) & (Regulon39, _llrD_)\$ [868] \\ \hline \multirow{3}{*}{_Lactococcus lactis_} & _dank_ & & _dank_ (llmg\_1574) & \\  & _groEL_ & & _groEL_ (llmg\_0411) & \\  & _groES_ & & _groES_ (llmg\_0410) & \\  & _grpE_ & & repair and protease & _grpE_ (llmg\_1575) & _llrA_ \\  & _clpE_ & & _clpE_ (llmg\_0528) & \\  & _clpC_ & & _clpC_ (llmg\_0615) & \\  & _clpP_ & & _clpP_ (llmg\_0638) & \\ \hline \multirow{3}{*}{_Lactococcus lactis_} & _dltc_, _agK_, & Envelope & & NHP6A, \\  & _SGP_, _fft_ & alterations & llmg\_0878 & _llrA_ \\ \hline \multirow{3}{*}{_Lactococcus lactis_} & _recA_, _uvr_, _smt_ & DNA repair & llmg\_0374, lmg\_0534, & (Regulon39, \\  & & & & llmg\_1718 llmg\_1221 & _llrD_)\$ [885] \\ \hline \end{tabular}
\end{table} 
Table 2: Known ASR-related gene mapping from literature in response to pH change. Literature-supported ASR-related genes found in close species or other _Lactococcus lactis_ strains. The template transporters and genes were first identified in published studies from the NCBI and UniProt databases. _Lactococcus lactis_ ll1403 was used as the organism which is very close to MG1363 if template gene existed. Only 36 templates that successfully mapped to the MG1363 genome were listed, which resulted in 33 genes. All mapped genes and corresponding templated were organized by their regulated pathways which were further used as functional modules. Mapped genes were searched in 51 regulons to build the connections between functional modules and regulons. Regulons _llrA_, _llrC_, and _hllA_ have already been computationally identified in Table 1 and supported again by literature verification results. The NHP6A gene, interestingly, has a homologous TF in humans and fungi but not in _L. lactis_[70; 71], yet failed to map in MG1363. Here, we are using NHP6A to represent regulon #20, as their relationship has been predicted computationally in Table 1. Regulon #39 was identified to be regulated by _llrD_, one of the six two-component regulatory systems in MG1363 [68].