TABLE 3.
Characteristics of ISLp11-related elements
| IS characteristics
|
Nucleic acid characteristicsa
|
Transposase size (aa) and/or comment | Source, reference, and/or database accession no. | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Name | Genetic linkage | Bacterial host | % Identity with ISLp11 | Size (bp) | Adjacent sequence | IR sequence (5′→3′) | IR size | Proposed target duplication (bp) | |||
| ISLp11 | ISLp12 on plasmid pLp3 | Lactobacillus plantarum HN38 | 100 | 1,043 | gtgt | GGTAGATTGTAAAATTAATCCGAA (IRL) | 24 | None | 309; functional | This work; EMBL AF459445 | |
| attc | GGTAGATTGCAAATTTAATCCGAA (IRR) | ||||||||||
| Chromosomal upp::ISLp11 | attc | 4 | This work | ||||||||
| gaat | |||||||||||
| iso-IS30 | tet(M) gene on plasmid pMD5057 | Lactobacillus plantarum 5057 | 99 | 1,051 | ttta | ATAT GGTAGATTGTAAAATTAATCCGAA (IRL) | 28 | ? | 309 | 8; GenBank AF440277 | |
| atct | ATAT GGTAGATTGCAAATTTAATCCAAA (IRR) | ||||||||||
| ISLP1 | Cold shock protein on plasmid pLF1 | Lactobacillus plantarum ATCC 14917 | 99 | 1,049 | ttga | AAT GGTAGATTGTAAAATTAATCCGAA (IRL) | 27 | None | 233; truncation due to TGA stop codon (positions 3139-3141) | Unpublished data; EMBL AF508808 | |
| aatg | AAT GGTAGATTGCAAATTTAATCCGAA (IRR) | ||||||||||
| Unnamed | Unknown | Oenococcus oeni MCW | 98 | 1,043 | tttt | GGTAGATTGTAAAATTAATCCGAA (IRL) | 24 | 4 | 309 | MCBI microbial genome annotation project | |
| aaaa | GGTAGATTGCAAATTTAATCCGAA (IRR) | ||||||||||
| iso-IS30 | Sucrose and raffinose operons | Pediococcus pentosaceus PPE1.0 | 98 | 1,041 | taca | TGGTAGATTGTAAAATTAATCCGA (IRL) | 24 | ? | 276; truncation due to 1-nt deletion in position 12233 | 18; EMBL Z32771 | |
| taat | TGGTAGATTGCAAATTTAATCCGA (IRR) | ||||||||||
| IS125 | Plantaricin 1.25β-encoding cluster | Lactobacillus plantarum TMW1.25 | 83 | 1,041 | attc | GGTAGATTGTAAAATTAATCCGAA (IRL) | 24 | 4 | 170; truncation due to 1-nt deletion in position 1841 | 9; EMBL AJ011094 | |
| gaat | GGTAGATTGCAAATTTAATCCGAA (IRR) | ||||||||||
| t GGTAGATTGTAAAATTAATCCGAa (IRL consensus) | |||||||||||
| t GGTAGATTGCAAATTTAATCCgAa (IRR consensus) | |||||||||||
a
The length of the IR was determined by analysis of the nucleotide identity between the ends of a given IS (nucleotides in upper case); nucleotides at the junction with the IS are indicated in lowercase italic characters; IR conserved nucleotides are indicated in bold; nucleotides which systematically differed between IRL and IRR are indicated by underlining in the consensus sequences; and the nucleotides found in at least half of the IS are indicated in lowercase bold characters.