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 AZPAE14693 | NQ90_RS11900 |
type VI secretion system protein ImpG
|
3 same-strain members: NQ90_RS00765 NQ90_RS11900 NQ90_RS25670 |
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Pseudomonas aeruginosa AZPAE14693 | NQ90_RS25670 |
type VI secretion system protein ImpG
|
3 same-strain members: NQ90_RS00765 NQ90_RS11900 NQ90_RS25670 |
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Pseudomonas aeruginosa AZPAE14809 | NR28_RS16530 |
type VI secretion protein
|
3 same-strain members: NR28_RS16530 NR28_RS23910 NR28_RS25560 |
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Pseudomonas aeruginosa AZPAE14809 | NR28_RS23910 |
type VI secretion system protein ImpG
|
3 same-strain members: NR28_RS16530 NR28_RS23910 NR28_RS25560 |
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Pseudomonas aeruginosa AZPAE14809 | NR28_RS25560 |
type VI secretion system protein ImpG
|
3 same-strain members: NR28_RS16530 NR28_RS23910 NR28_RS25560 |
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Pseudomonas aeruginosa AZPAE14817 | NR36_RS25120 |
type VI secretion system protein ImpG
|
3 same-strain members: NR36_RS25120 NR36_RS25640 NR36_RS05385 |
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Pseudomonas aeruginosa AZPAE14817 | NR36_RS25640 |
type VI secretion protein
|
3 same-strain members: NR36_RS25120 NR36_RS25640 NR36_RS05385 |
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Pseudomonas aeruginosa AZPAE14817 | NR36_RS05385 |
type VI secretion system protein ImpG
|
3 same-strain members: NR36_RS25120 NR36_RS25640 NR36_RS05385 |
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Pseudomonas aeruginosa AZPAE14825 | NR43_RS00735 |
type VI secretion protein
|
3 same-strain members: NR43_RS00735 NR43_RS22145 NR43_RS23565 |
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Pseudomonas aeruginosa AZPAE14825 | NR43_RS22145 |
type VI secretion system protein ImpG
|
3 same-strain members: NR43_RS00735 NR43_RS22145 NR43_RS23565 |
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Pseudomonas aeruginosa AZPAE14825 | NR43_RS23565 |
type VI secretion system protein ImpG
|
3 same-strain members: NR43_RS00735 NR43_RS22145 NR43_RS23565 |
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Pseudomonas aeruginosa AZPAE14840 | NR58_RS00250 |
type VI secretion system protein ImpG
|
3 same-strain members: NR58_RS00250 NR58_RS13945 NR58_RS18665 |
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Pseudomonas aeruginosa AZPAE14840 | NR58_RS13945 |
type VI secretion system protein ImpG
|
3 same-strain members: NR58_RS00250 NR58_RS13945 NR58_RS18665 |
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Pseudomonas aeruginosa AZPAE14840 | NR58_RS18665 |
type VI secretion protein
|
3 same-strain members: NR58_RS00250 NR58_RS13945 NR58_RS18665 |
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|
Pseudomonas aeruginosa AZPAE14842 | NR60_RS14500 |
type VI secretion system protein ImpG
|
3 same-strain members: NR60_RS14500 NR60_RS27880 NR60_RS30380 |
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Pseudomonas aeruginosa AZPAE14842 | NR60_RS27880 |
type VI secretion protein
|
3 same-strain members: NR60_RS14500 NR60_RS27880 NR60_RS30380 |
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Pseudomonas aeruginosa AZPAE14842 | NR60_RS30380 |
type VI secretion system protein ImpG
|
3 same-strain members: NR60_RS14500 NR60_RS27880 NR60_RS30380 |
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Pseudomonas aeruginosa AZPAE14847 | NR65_RS13210 |
type VI secretion system protein ImpG
|
3 same-strain members: NR65_RS13210 NR65_RS21830 NR65_RS23360 |
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Pseudomonas aeruginosa AZPAE14847 | NR65_RS21830 |
type VI secretion protein
|
3 same-strain members: NR65_RS13210 NR65_RS21830 NR65_RS23360 |
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Pseudomonas aeruginosa AZPAE14847 | NR65_RS23360 |
type VI secretion system protein ImpG
|
3 same-strain members: NR65_RS13210 NR65_RS21830 NR65_RS23360 |
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