What's a Pseudomonas Ortholog Group?

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.

Pseudomonas Ortholog Group POG000219

3043 results were returned for your query
= Popular strains (Ordered by popular strains first, then by strain name, ascending)
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
Pseudomonas fluorescens SS101 PflSS101_4543 amino acid permease
4 same-strain members:
PflSS101_0391
PflSS101_1110
PflSS101_2593
PflSS101_4543
Pseudomonas fluorescens SS101 PflSS101_0391 permease
4 same-strain members:
PflSS101_0391
PflSS101_1110
PflSS101_2593
PflSS101_4543
Pseudomonas fluorescens SS101 PflSS101_1110 alanine glycine permease
4 same-strain members:
PflSS101_0391
PflSS101_1110
PflSS101_2593
PflSS101_4543
Pseudomonas fluorescens UK4 HZ99_RS04930 amino acid transporter
3 same-strain members:
HZ99_RS04930
HZ99_RS11250
HZ99_RS19490
Pseudomonas fluorescens UK4 HZ99_RS11250 D-alanine/D-serine/glycine permease
3 same-strain members:
HZ99_RS04930
HZ99_RS11250
HZ99_RS19490
Pseudomonas fluorescens UK4 HZ99_RS19490 proline-specific permease
proY
3 same-strain members:
HZ99_RS04930
HZ99_RS11250
HZ99_RS19490
Pseudomonas frederiksbergensis SI8 - Assembly GCF_000802155.2 JZ00_RS14445 D-alanine/D-serine/glycine permease
2 same-strain members:
JZ00_RS14445
JZ00_RS28540
Pseudomonas frederiksbergensis SI8 - Assembly GCF_000802155.2 JZ00_RS28540 amino acid permease
2 same-strain members:
JZ00_RS14445
JZ00_RS28540
Pseudomonas fulva 12-X Psefu_1604 amino acid permease
1 member
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
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
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
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
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
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
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
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
Pseudomonas helleri DSM 29165 TU84_RS02825 amino acid permease
2 same-strain members:
TU84_RS02825
TU84_RS02855
Pseudomonas helleri DSM 29165 TU84_RS02855 D-alanine/D-serine/glycine permease
2 same-strain members:
TU84_RS02825
TU84_RS02855