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Fig. 1 | AMB Express

Fig. 1

From: Development of whole-cell catalyst system for sulfide biotreatment based on the engineered haloalkaliphilic bacterium

Fig. 1

Bioinformatic analysis of sulfide oxidation genes from microbial metagenomes of soda-saline lakes. a Phylogenetic analysis of sulfide: quinone oxidoreductase (Sqr) and flavocytochrome c: sulfide dehydrogenase (FCSD). The sequences were obtained from previous research (Zhao et al. 2020). The evolutionary tree was inferred by using the Maximum Likelihood method and JTT matrix-based model (Jones et al. 1992). The tree with the highest log likelihood (-644966.85) is shown. Initial trees for the heuristic search were automatically obtained by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the JTT model. Then, the topology with a superior log-likelihood value was selected. There were 986 positions in the final dataset. This analysis involved 484 sulfide oxidases and 33 reference sequences indicated by red branches (All sequence data shown in Additional file 1: Table S1). The outer circle was colored by different Sqr types and FCSD. The positions of the top five Sqrs in abundance were marked with blue five-pointed stars. The blue numbers (1 to 5) were the abundance rankings corresponding to those in Fig. 1b and c. b The percentage of the total abundance of the proteins in 18 samples. The abundance data were described in previous work (Zhao et al. 2020) and were shown in Additional file 1: Table S2. c Maximum Likelihood phylogenetic tree based on the Sqr of Spiribacter sp. IM2438 and the partial type II Sqrs in Fig. 1a (20 protein sequence names shown in red in Additional file 1: Table S1). Bootstrap values (%) were based on 1000 replicates and depicted with more than 70 % bootstrap support. NCBI reference accession numbers are shown in parentheses. Bar, 0.01 substitutions per nucleotide position

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