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 ? | |
---|---|---|---|---|---|
Pseudomonas aeruginosa Z61 | Q054_05813 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas alcaliphila 34 | D567_RS0107900 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas alkylphenolia KL28 | PSAKL28_RS26195 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas amygdali pv. tabaci ATCC 11528 - Assembly GCF_001006455.1 | AAY86_RS22555 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas brassicacearum 51MFCVI2.1 | PSBVI21_RS0128480 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas brassicacearum DF41 | CD58_RS28525 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas brassicacearum PA1G7 | AW28_RS20340 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas brassicacearum PP1_210F | P908_RS02870 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas brassicacearum subsp. brassicacearum NFM421 | PSEBR_a5613 |
cardiolipin synthase
|
1 member |
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|
Pseudomonas chlororaphis EA105 | NZ35_RS05920 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas chlororaphis HT66 | M217_RS0116920 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas chlororaphis O6 | PchlO6_6262 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas chlororaphis PA23 | EY04_RS29120 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas chlororaphis PCL1606 | PCL1606_RS00160 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas chlororaphis subsp. aurantiaca JD37 | JM49_RS00425 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas chlororaphis subsp. aureofaciens 30-84 | PCHL3084_RS00450 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas chlororaphis subsp. aureofaciens NBRC 3521 | PCH03S_RS22685 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas chlororaphis UFB2 isolate Soil | VM99_RS00070 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas chlororaphis YL-1 | P637_RS0124790 |
cardiolipin synthetase
|
1 member |
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|
Pseudomonas cichorii JBC1 | BH81_RS25555 |
cardiolipin synthetase
|
1 member |
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