Table 3.

Properties of Vibrio fischeriSuperintegron 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/activity[vii]
p667 + p641 inserts[viii]
 c667-1<1–39——[ix] ——
 c667-2* 40–601 98ND—BLASTX detects a 56-codon seqment that shows homology  to intron maturase
 c667-3* 602–1161 99ND——
 c667-4* 1162–1724 98ND——
 c667-5/c641-11725–3415116Orfc667-5/153929.4NH—3 transmembrane helices
 c641-23416–4070116Orfc641-2/42635.740% identity to the Yersinia pestis putative acetyltransferase  CAC93527 (E = 4e − 24)
 c641-34071–4123>—ND—NH
p668 insert
 c668-11–686118Orfc668-1/51339.039% identity to the V. choleraeVCA1017methylated- DNA–protein-cysteine S-methyltransferase hypothetical  OGT (E = 3e − 22)
 c668-2* 687–1264117ND—
 c668-31265–1780116Orfc668-3[x]/14734.0NH
 c668-4* 1781–2339 97ND——
 c668-52340–3251116Orfc668-5/75631.7NH—signal peptide—2 transmembrane helices
 c668-63552–4003>—Orfc668-6/711>30.2NH
p669 insert
 c669-1<1–404116Orfc669-1/<28033.3NH—1 transmembrane helix
 c669-2405–1145118 CcdB/315   CcdA/24633.3   34.2 Gyrase inhibiting protein, 42% identity to the F plasmid  CcdB CcdB antidote, 42% identity to Escherichia coli O157:H7  CcdA (AE005182.1)
 c669-31146–1910118Orfc669-3/61533.340% identity to Bacillus halodurans transcriptional repressor  of sporulation and degradative enzymes production  NP_241278 (E = 2e − 35)
 c669-41911–3268116Orfc669-4/120034.937% identity to the N-terminal 240 aa of Streptomyces  coelicolor Serine/threonine protein kinase T36502  (E = 1e − 30)
 c669-5* 3269–3829 98———
 c669-6** 3830–4483>—Orfc669-6/632>34.3NH
p672 insert
 c672-1<1–79——[ix] ——
 c672-280–682116Orfc672-2/44435.628% identity to the S. coelicolor putative acetyl transferase  (E = 1e − 07)
 c672-3* 683–1260117ND——
 c672-41261–2254118Orfc672-4/843>39.3NH—signal peptide sequence—2 transmembrane helices
 c672-5* 2255–2813 98ND——
 c672-62814–3438>—Orfc672-6/605>33.6NH
p789 insert
 c789-11974–2679116Orfc789-1/51329.540% identity to the V. cholerae VCA0405 60 N-terminal  amino acids and 35% identity to the Lactococcus lactis  prophage pi2 protein 2 (AE006335_3) 75 C-terminal  amino acids—signal peptide sequence—2 transmembrane  helices
 c789-2** 2680–3028>—Orfc789-2/327>33.7NH (identical to c669-6)

[i] Cassettes (c) have been named according to their plasmid number (see Table 1) and their position in the insert; 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] Demonstrated activities are in bold characters. 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 p667 and p641 inserts overlapping each other, we have annotated and deposited to GenBank the corresponding contig.

[ix] Irrelevant, as the sequence only corresponds to the 3′ part of the attC site.

[x] This 147-bp ORF is preceded by a canonical ribosome-binding site and consequently has been considered as a potential gene.