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 putida S13.1.2 - Assembly GCF_000498395.2 | N805_RS13700 |
Cro/Cl family transcriptional regulator
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2 same-strain members: N805_RS09535 N805_RS13700 |
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Pseudomonas putida S16 | PPS_2197 |
XRE family transcriptional regulator
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2 same-strain members: PPS_2197 PPS_2534 |
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Pseudomonas putida S16 | PPS_2534 |
XRE family transcriptional regulator
|
2 same-strain members: PPS_2197 PPS_2534 |
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Pseudomonas putida YKD221 | TR32_RS15850 |
Cro/Cl family transcriptional regulator
|
2 same-strain members: TR32_RS15850 TR32_RS03865 |
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Pseudomonas putida YKD221 | TR32_RS03865 |
Cro/Cl family transcriptional regulator
|
2 same-strain members: TR32_RS15850 TR32_RS03865 |
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Pseudomonas resinovorans DSM 21078 | G559_RS0126455 |
Cro/Cl family transcriptional regulator
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2 same-strain members: G559_RS0126455 G559_RS0123750 |
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Pseudomonas resinovorans DSM 21078 | G559_RS0123750 |
Cro/Cl family transcriptional regulator
|
2 same-strain members: G559_RS0126455 G559_RS0123750 |
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Pseudomonas resinovorans NBRC 106553 | PCA10_RS02470 |
transcriptional regulator
|
2 same-strain members: PCA10_RS02470 PCA10_RS26015 |
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Pseudomonas resinovorans NBRC 106553 | PCA10_RS26015 |
transcriptional regulator
|
2 same-strain members: PCA10_RS02470 PCA10_RS26015 |
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Pseudomonas simiae 2-36 | LS88_RS18385 |
Cro/Cl family transcriptional regulator
|
1 member |
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Pseudomonas simiae MEB105 | RU03_RS13730 |
Cro/Cl family transcriptional regulator
|
1 member |
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Pseudomonas simiae WCS417 | PS417_RS17410 |
Cro/Cl family transcriptional regulator
|
1 member |
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Pseudomonas sp. 11/12A | GQ39_RS09730 |
Cro/Cl family transcriptional regulator
|
2 same-strain members: GQ39_RS09730 GQ39_RS12185 |
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Pseudomonas sp. 11/12A | GQ39_RS12185 |
Cro/Cl family transcriptional regulator
|
2 same-strain members: GQ39_RS09730 GQ39_RS12185 |
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Pseudomonas sp. 2-92 | U367_RS0128545 |
Cro/Cl family transcriptional regulator
|
2 same-strain members: U367_RS0128545 U367_RS0128710 |
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Pseudomonas sp. 2-92 | U367_RS0128710 |
Cro/Cl family transcriptional regulator
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2 same-strain members: U367_RS0128545 U367_RS0128710 |
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Pseudomonas sp. 21 | UB43_RS23805 |
Cro/Cl family transcriptional regulator
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2 same-strain members: UB43_RS23805 UB43_RS15860 |
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Pseudomonas sp. 21 | UB43_RS15860 |
Cro/Cl family transcriptional regulator
|
2 same-strain members: UB43_RS23805 UB43_RS15860 |
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Pseudomonas sp. AAC | FG99_RS10300 |
Cro/Cl family transcriptional regulator
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2 same-strain members: FG99_RS07525 FG99_RS10300 |
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Pseudomonas sp. AAC | FG99_RS07525 |
XRE family transcriptional regulator
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2 same-strain members: FG99_RS07525 FG99_RS10300 |
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