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 POG000081

1178 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 chlororaphis UFB2 isolate Soil VM99_RS27195 type VI secretion protein ImpA
3 same-strain members:
VM99_RS02015
VM99_RS22970
VM99_RS27195
Pseudomonas chlororaphis YL-1 P637_RS0125160 type VI secretion protein ImpA
2 same-strain members:
P637_RS0125160
P637_RS0107970
Pseudomonas chlororaphis YL-1 P637_RS0107970 type VI secretion protein ImpA
2 same-strain members:
P637_RS0125160
P637_RS0107970
Pseudomonas cichorii JBC1 BH81_RS10575 type VI secretion protein
2 same-strain members:
BH81_RS10575
BH81_RS12860
Pseudomonas cichorii JBC1 BH81_RS12860 type VI secretion protein ImpA
2 same-strain members:
BH81_RS10575
BH81_RS12860
Pseudomonas cremoricolorata DSM 17059 H618_RS0101215 type VI secretion protein ImpA
1 member
Pseudomonas cremoricolorata ND07 LK03_RS04705 type VI secretion protein ImpA
1 member
Pseudomonas denitrificans ATCC 13867 H681_03925 hypothetical protein
2 same-strain members:
H681_03925
H681_14855
Pseudomonas denitrificans ATCC 13867 H681_14855 hypothetical protein
2 same-strain members:
H681_03925
H681_14855
Pseudomonas entomophila L48 PSEEN0522 hypothetical protein
1 member
Pseudomonas fluorescens AU10414 AA048_RS09250 type VI secretion protein ImpA
1 member
Pseudomonas fluorescens AU10973 MZ33_RS26560 type VI secretion protein ImpA
1 member
Pseudomonas fluorescens AU11122 AA047_RS06530 type VI secretion protein ImpA
1 member
Pseudomonas fluorescens AU11136 AA055_RS08335 type VI secretion protein ImpA
1 member
Pseudomonas fluorescens AU11164 AA046_RS08115 type VI secretion protein ImpA
1 member
Pseudomonas fluorescens AU11235 AA056_RS07530 type VI secretion protein ImpA
1 member
Pseudomonas fluorescens AU12597 AA053_RS08210 type VI secretion protein ImpA
1 member
Pseudomonas fluorescens AU12644 AA054_RS04260 type VI secretion protein ImpA
1 member
Pseudomonas fluorescens AU13852 AA097_RS17870 type VI secretion protein ImpA
2 same-strain members:
AA097_RS28595
AA097_RS17870
Pseudomonas fluorescens AU13852 AA097_RS28595 type VI secretion protein ImpA
2 same-strain members:
AA097_RS28595
AA097_RS17870