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 fluorescens SS101 | PflSS101_2593 |
amino acid ABC transporter permease
puuP |
4 same-strain members: PflSS101_0391 PflSS101_1110 PflSS101_2593 PflSS101_4543 |
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Pseudomonas fluorescens SS101 | PflSS101_4543 |
amino acid permease
|
4 same-strain members: PflSS101_0391 PflSS101_1110 PflSS101_2593 PflSS101_4543 |
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Pseudomonas fluorescens SS101 | PflSS101_0391 |
permease
|
4 same-strain members: PflSS101_0391 PflSS101_1110 PflSS101_2593 PflSS101_4543 |
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Pseudomonas fluorescens SS101 | PflSS101_1110 |
alanine glycine permease
|
4 same-strain members: PflSS101_0391 PflSS101_1110 PflSS101_2593 PflSS101_4543 |
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Pseudomonas fluorescens UK4 | HZ99_RS04930 |
amino acid transporter
|
3 same-strain members: HZ99_RS04930 HZ99_RS11250 HZ99_RS19490 |
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Pseudomonas fluorescens UK4 | HZ99_RS11250 |
D-alanine/D-serine/glycine permease
|
3 same-strain members: HZ99_RS04930 HZ99_RS11250 HZ99_RS19490 |
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Pseudomonas fluorescens UK4 | HZ99_RS19490 |
proline-specific permease
proY |
3 same-strain members: HZ99_RS04930 HZ99_RS11250 HZ99_RS19490 |
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Pseudomonas frederiksbergensis SI8 - Assembly GCF_000802155.2 | JZ00_RS14445 |
D-alanine/D-serine/glycine permease
|
2 same-strain members: JZ00_RS14445 JZ00_RS28540 |
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Pseudomonas frederiksbergensis SI8 - Assembly GCF_000802155.2 | JZ00_RS28540 |
amino acid permease
|
2 same-strain members: JZ00_RS14445 JZ00_RS28540 |
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Pseudomonas fulva 12-X | Psefu_1604 |
amino acid permease
|
1 member |
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Pseudomonas fulva NBRC 16636 = DSM 17004 - Assembly GCF_000621265.1 | Q382_RS0109130 |
amino acid permease
|
4 same-strain members: Q382_RS0103165 Q382_RS0109130 Q382_RS0110925 Q382_RS0112310 |
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Pseudomonas fulva NBRC 16636 = DSM 17004 - Assembly GCF_000621265.1 | Q382_RS0110925 |
proline-specific permease
proY |
4 same-strain members: Q382_RS0103165 Q382_RS0109130 Q382_RS0110925 Q382_RS0112310 |
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Pseudomonas fulva NBRC 16636 = DSM 17004 - Assembly GCF_000621265.1 | Q382_RS0112310 |
Putrescine importer PuuP
|
4 same-strain members: Q382_RS0103165 Q382_RS0109130 Q382_RS0110925 Q382_RS0112310 |
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Pseudomonas fulva NBRC 16636 = DSM 17004 - Assembly GCF_000621265.1 | Q382_RS0103165 |
Putrescine importer PuuP
|
4 same-strain members: Q382_RS0103165 Q382_RS0109130 Q382_RS0110925 Q382_RS0112310 |
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Pseudomonas fulva NBRC 16636 = DSM 17004 - Assembly GCF_000730565.1 | PFU01S_RS14890 |
putrescine importer PuuP
|
4 same-strain members: PFU01S_RS14890 PFU01S_RS11860 PFU01S_RS08415 PFU01S_RS02050 |
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Pseudomonas fulva NBRC 16636 = DSM 17004 - Assembly GCF_000730565.1 | PFU01S_RS11860 |
proline-specific permease
proY |
4 same-strain members: PFU01S_RS14890 PFU01S_RS11860 PFU01S_RS08415 PFU01S_RS02050 |
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Pseudomonas fulva NBRC 16636 = DSM 17004 - Assembly GCF_000730565.1 | PFU01S_RS08415 |
amino acid permease
|
4 same-strain members: PFU01S_RS14890 PFU01S_RS11860 PFU01S_RS08415 PFU01S_RS02050 |
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Pseudomonas fulva NBRC 16636 = DSM 17004 - Assembly GCF_000730565.1 | PFU01S_RS02050 |
putrescine importer PuuP
|
4 same-strain members: PFU01S_RS14890 PFU01S_RS11860 PFU01S_RS08415 PFU01S_RS02050 |
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Pseudomonas helleri DSM 29165 | TU84_RS02825 |
amino acid permease
|
2 same-strain members: TU84_RS02825 TU84_RS02855 |
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Pseudomonas helleri DSM 29165 | TU84_RS02855 |
D-alanine/D-serine/glycine permease
|
2 same-strain members: TU84_RS02825 TU84_RS02855 |
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