Properties of Vibrio metschnikoviiSuperintegron Cassettes
| Gene cassette[i] | Cassette coordinates[ii] (bp) | Length of attC site[iii](bp) | Name[iv]/length of ORF (bp) | G + C content of ORF (%) | Sequence similarity,[v] E-value,[vi] and motifs[vii] |
| p253 insert | |||||
| c253-1* | <1–987[viii] | 117 | ND | — | (ISVme1 insertion) |
| c253-2 | 988–1531 | 116 | Orfc253-2/387 | 37.2 | 70% identity to the V. cholerae VCA0890 Glyoxylase I family protein |
| c253-3 | 1532–2036 | 118 | Orfc253-3/360 | 40.1 | 94% identity to the V. cholerae VCA0338 andVC0415 |
| c253-4 | 2037–2825 | 117 | Orfc253-4/642 | 36.6 | NH—1 transmembrane helix |
| c253-5 | 2826–3373 | 118 | Orfc253-5/396 | 39.4 | 66% identity to the V. cholerae VCA0414 andVC0425 signal peptide sequence |
| c253-6 | 3374–3926> | — | Orfc253-6a/171 | 39.3 | 100% identity to the V. cholerae VCA0474 C-terminal 56 aa, see text. |
| Orfc253-6b/320> | 42.5 | 99% identity to the V. cholerae VCA0475 (30% identity to Phage P1Doc) | |||
| p273 insert | |||||
| c273-1 | <1–490 | 118 | Orfc273-1/<375 | 38.7 | 48% identity to the C-terminal part of Bacillus halodurans hypothetical protein BH3804 (E = 7e − 6) |
| c273-2* | 491–992 | 117 | ND | — | — |
| c273-3 | 993–1697 | 118 | Orfc273-3/558 | 38.0 | NH |
| c273-4 | 1698–2385 | 118 | Orfc273-4/336 | 49.4 | NH |
| c273-5 | 2386–3367 | 117 | Orfc273-5/837 | 36.9 | 22% identity to HphI restriction endonuclease (E = 4e − 8) |
| c273-6* | 3368–4055 | 117 | ND | — | — |
| c273-7 | 4056–4557> | — | Orfc273-7/361> | 31.7 | NH—signal peptide sequence |
| p372 insert | |||||
| c372-1 | <1–821 | 118 | Orfc372-1/<689 | 31.7 | NH |
| c372-2 | 822–1316 | 117 | Orfc372-2/291 | 34.7 | 34% identity to Salmonella enterica hypothetical protein CAD05348 (E = 0.01)—signal peptide sequence |
| c372-3 | 1317–2077 | 117 | Orfc372-3/609 | 35.3 | NH—signal peptide sequence—6 transmembrane helices |
| c372-4 | 2078–2931 | 118 | Orfc372-4/708 | 36.6 | 40% identity to the Salmonella typhimurium LT2 putative aspartate racemase AAL21891 (E = 7e − 41) |
| c372-5* | 2932–3621 | 117 | ND | — | — |
| c372-6 | 3622–4242>[ix] | — | ND | — | (ISVme1 insertion) |
| p374 insert | |||||
| c374-1 | 658–1711 | 117 | Orfc374-1/879 | 34.0 | NH |
| c374-2** | 1712–2607 | 118 | Orfc374-2/669 | 38.9 | 20.5% identity to Lactococcus lactis methyltransferase CAA68045 (E = 0.001) |
| c374-3 | 2608–3383 | 117 | Orfc374-3/633 | 36.8 | 26.3% identity to Agrobacterium tumefaciens hypothetical methyltransferase AAK87648 (E = 3e − 13) |
| 374-4** | 3384–4279 | 118 | Orfc374-4/669 | 39.3 | 98% identity to c374-2 |
| c374-5 | 4280–5137 | 118 | Orfc374-5/705 | 36.3 | NH |
| c374-6 | 5138–5601 | 116 | ND | — | — |
| c374-7 | 5602–6437> | — | Orfc374-7/771 | 40.6 | 29% identity to Sinorhizobium meliloti hypothetical oxydoreductase CAC46573 (E = 7e − 22) |
| PCR (VMR1 + VMR2) | |||||
| Vme1 | 1–437> | / | OrfVme1/396 | 39.4 | 100% identity to c253-5 |
| Vme2 | 1–578> | / | OrfVme2a/267 OrfVme2b/243 | 39.1 40.0 | 92% identity to the V. cholerae VCA0332 82% identity to V. cholerae VCA0333 |
| Vme4* | 1–393> | / | ND | — | — |
| Vme9 | 1–502> | / | OrfVme9/375 | 33.6 | 46% identity between the last 40 C-terminal aa and a central segment of chicken paxillin B55933—signal peptide sequence—2 transmembrane helices |
| Vme11 | 1–496> | / | OrfVme11/414 | 41.3 | 91% identity to the V. cholerae VCA0476 |
| Vme12 | 1–335> | / | OrfVme12/198 | 34.9 | 36% identity to the V. cholerae VCA0426(E = 4e − 6) |
| Vme23* | 1–394> | / | ND | — | — |
[i] Cassettes (c) have been named according to their plasmid number (see Table 1) and their position in the insert, or for the cassette obtained from (VMR1 + VMR2) PCR by the prefix Vme followed of a number; the two families of repeated cassettes are indicated by * and **, respectively.
[ii] Sequences missing 5′ or 3′ in incomplete cassettes are indicated by < and >, respectively.
[iii] The given attC site length is from the last Y of the inverse core site (RYYYAAC) to the G located upstream of the recombination point in the core site of the integrated cassette (GTTRRRY).
[iv] ORFs are in classical positive orientation that is in the same direction as their associated attC site. ORFs in the opposite orientations are underlined; ND, no ORF > 150-bp detected.
[v] NH, no homologous protein detected by BLAST analysis (http://www.ncbi.nlm.nih.gov/BLAST/). When related to a V. cholerae SI cassette, the corresponding VCAxxx name is underlined.
[vi] Number of equal scoring matches expected by chance, results with value ≤10−2 have been considered.
[vii] Motifs have been evidenced through the CDD search option in BLAST analysis and by using the signal peptide and transmembrane segment prediction programs SignalP and TMHMM (Center for Biological Sequence Analysis; http://www.cbs.dtu.dk/services/).
[viii] The sequence from 1 to 540 corresponds to a never described IS, ISVme1.
[ix] The sequence from 3703 to the end corresponds to an ISVme1, identical to the one found in cassette c253-1.