Table 1 List of genes and classification of encoded proteins according to replication- related Pfam numbers.
From: Genomics of high molecular weight plasmids isolated from an on-farm biopurification system
Pfam number | Pfam ID | Description | Different proteins | Organism | % Identity to the closest protein |
|---|---|---|---|---|---|
pfam00436 | SSB | Single-strand binding protein family | 10 | Legionella pneumophila | 50% |
Legionella shakespearei | 49% | ||||
Ottowia thiooxydans | 96% | ||||
Pseudomonas putida | 99% | ||||
Ochrobactrum intermedium | 93% | ||||
Microbacterium yannicii | 52% | ||||
Pseudomonas syringae | 86% | ||||
Acinetobacter baumannii | 99% | ||||
Pseudomonas putida | 59% | ||||
Salmonella enterica | 100% | ||||
pfam01051 | Rep_3 | Initiator Replication protein | 6 | Providencia alcalifaciens | 64% |
Salmonella enterica | 99% | ||||
Pseudomonas putida | 100% | ||||
Pseudomonas taiwanensis | 71% | ||||
Salmonella enterica | 99% | ||||
Pseudomonas taiwanensis | 99% | ||||
pfam02486 | Rep_trans | Replication initiation factor | 5 | Acidovorax citrulli | 56% |
Streptococcus parasanguinis | 97% | ||||
Acidovorax delafieldii | 48% | ||||
Streptococcus parasanguinis | 97% | ||||
Acidovorax citrulli | 56% | ||||
pfam11740 | KfrA_N | Plasmid replication region DNA-binding N-term | 5 | Pseudomonas aeruginosa | 100% |
Pseudomonas putida | 46% | ||||
Serratia marcescens | 89% | ||||
Salmonella enterica | 100% | ||||
Pseudomonas sp. | 100% | ||||
pfam11800 | RP-C_C | Replication protein C C-terminal region | 5 | Ochrobactrum anthropi | 83% |
Ochrobactrum anthropi | 89% | ||||
Ochrobactrum rhizosphaerae | 99% | ||||
Sinorhizobium meliloti | 94% | ||||
Ochrobactrum anthropi | 88% | ||||
pfam03428 | RP-C | Replication protein C N-terminal domain | 4 | Ochrobactrum rhizosphaerae | 88% |
Sinorhizobium meliloti | 94% | ||||
Ochrobactrum rhizosphaerae | 95% | ||||
Ochrobactrum rhizosphaerae | 94% | ||||
pfam04796 | RepA_C | Plasmid encoded RepA protein | 3 | uncultured bacterium | 62% |
uncultured bacterium | 53% | ||||
Enterobacteriaceae | 100% | ||||
pfam07042 | trfA | TrfA protein | 2 | Thauera terpenica | 68% |
Pseudomonadales | 100% | ||||
pfam05472 | Ter | DNA replication terminus site-binding protein (Ter protein) | 2 | Escherichia coli | 99% |
Pseudomonas sp. | 100% | ||||
pfam01446 | Rep_1 | Replication protein | 2 | Bacillus pumilus | 94% |
Bacillus pumilus | 98% | ||||
pfam03090 | Replicase | Replicase family | 2 | Pseudomonas sp. | 90% |
Aeromonas hydrophila | 99% | ||||
pfam06504 | RepC | Replication protein C (RepC) | 1 | Pseudomonas aeruginosa | 96% |
pfam02387 | IncFII_repA | IncFII RepA protein family | 1 | Klebsiella pneumoniae | 96% |
