In order to generate a more inclusive dataset of Pseudomonas genes mapped to putative in-paralogs and putative orthologs in other Pseudomonas species/strains, we developed a Pseudomonas Orthologous Groups classification system.
To generate ortholog groups, pair-wise DIAMOND searches were run on all genomes in the database to find reciprocal best hits (RBHs) for each gene. These analyses often resulted in multiple candidate genes for RBH status, which were narrowed down by examining the similarity between the query's flanking genes and the hit's flanking genes. If two candidate genes were directly adjacent, they where both accepted as RBHs that involve putative in-parology.
Pairwise intra-genome DIAMOND searches were also performed to acquire in-paralog information (i.e. gene duplications occurring after species divergence). If two genes in one genome were reciprocally more similar to each other than to any gene in the other genomes, the two genes were designated putative in-paralogs. Ortholog groups are built by starting with a seed gene and then adding all genes to which there is a RBH or in-paralog relationship.
Every new gene added to an ortholog group was then treated as a seed gene and the addition process was repeated until all qualifying genes had been added. The result was the development of orthologous groups, specifically generated for Pseudomonas species genomes, which can be used to sort search results.
Strain | Locus Tag | Description | Same-Strain Members | Fragment ? | |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_29_a1 | TC72_RS26840 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS26815 TC72_RS26840 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_2_a1 | TC72_RS17705 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS17705 TC72_RS17730 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_2_a1 | TC72_RS17730 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS17705 TC72_RS17730 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_30_a1 | TC72_RS26295 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS26295 TC72_RS26320 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_30_a1 | TC72_RS26320 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS26295 TC72_RS26320 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_31_a1 | TC72_RS25490 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS25490 TC72_RS25515 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_31_a1 | TC72_RS25515 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS25490 TC72_RS25515 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_32_a1 | TC72_RS23345 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS23345 TC72_RS23370 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_32_a1 | TC72_RS23370 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS23345 TC72_RS23370 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_33_a1 | TC72_RS19735 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS19735 TC72_RS19760 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_33_a1 | TC72_RS19760 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS19735 TC72_RS19760 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_34_a1 | TC72_RS19025 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS19025 TC72_RS19050 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_34_a1 | TC72_RS19050 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS19025 TC72_RS19050 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_35_a1 | TC72_RS24830 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS24805 TC72_RS24830 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_35_a1 | TC72_RS24805 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS24805 TC72_RS24830 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_36_a1 | TC72_RS22275 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS22275 TC72_RS22300 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_36_a1 | TC72_RS22300 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS22275 TC72_RS22300 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_37_a1 | TC72_RS17590 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS17590 TC72_RS17615 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_37_a1 | TC72_RS17615 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS17590 TC72_RS17615 |
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Pseudomonas aeruginosa LES_CF_sputum_CF03_contigs_38_a1 | TC72_RS26810 |
Fis family transcriptional regulator
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2 same-strain members: TC72_RS26810 TC72_RS26835 |
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