TABLE 3.
Sequence analysis of 19-kb region of CTnGERM1
| Location bp-bp 5′-3′ | ORF or designation | No. of aa | % aa identity (no. of aa involved/total no. of aa) | Results and descriptions of BLAST searches (accession no.) |
|---|---|---|---|---|
| 1009-1368 | 1 | 119 | 32 (16/50) | Rhizobium melioti NodM (606 aa) homology in C-terminal end (X58632) |
| 1556-2785 | tnpIS | 409 | 90 (369/409) | Bacteroides fragilis transposase (428 aa) of IS613 and closely related IS elements in imipenem-resistant strains (BAA95632.1). This protein is missing first 20 aa. There is 92% identity at the nucleotide level. Contains transposase DDE domain of the IS4 group. There are other related Bacteroides insertion elements. |
| 4006-4240 | 3 | 121 | 35 (33/93) | B. fragilis Orf9 (481 aa) of unknown function located on mobilizable transposon Tn4555 (AAD43601) |
| 5259-4764 | 4 | 164 | 58 (94/162) | Desulfitobacterium hafniense (181 aa) hypothetical protein (00098450.1); Clostridium acetobutylicum HD superfamily hydrolase (163 aa, AE007856). The translated orf4 protein has the HD and HDc motifs for metal-dependent phosphohydrolases. |
| 5260-6290 | orfY′ and C′-orfX | 230 | 85 (204/243) | Staphylococcus intermedius OrfY (244 aa) of unknown function. Associated with ermB and other antibiotic resistance genes (AF299292). The nucleotide identity is ∼92%. There is a frameshift in the sequence. The 220 nucleotides of the 3′ end of the upstream orfX (unknown function) are also present. These genes are also found on the Enterococcus faecium plasmid pUW786 (17,510 bp) that contains ermB and vancomycin resistance genes (AF516335). OrfX and OrfY are carried on Tn5404/Tn5405 originally isolated in Staphylococcus (4). |
| 6631-7365 | ermG | 244 | 99 (236/239) | Bacillus sphaericus ErmG (244 aa) on a plasmid (M15332). >99% identical at the nucleotide level. Also found on Bacteroides CTn7853 (L42817). |
| 7366-7860 | 7 | 125 | 33 (50/161) | Bacillus firmus glutamine-rich protein (AAB05373.1) |
| 9420-8137 | ABC transporter or mel | 428 | 97 (414/427) | Streptococcus pneumoniae Mel (487 aa), a homolog of the product of the macrolide-streptogramin B efflux resistance gene msr(SA) (AAK69028). Has 96% nucleotide identity. Called an ABC transporter or orf5 on Tn1207.1 (15). Located downstream of mefA. Protein missing N-terminal end due to nonsense mutations. |
| 10854-9922 | mefA | 310 | 86 (248/287) | Streptococcus pyogenes MefA (405 aa) macrolide-cfflux protein (AAC44785). 94% nucleotide identity. There are two stop codons in the end corresponding to the N terminus. Also found on Tn1207.1 in an S. pneumoniae clinical strain (15) situated upstream of ABC transporter or mel. This MefA protein is missing the N-terminal end due to nonsense mutations. |
| 12895-11537 | orf10 | 452 | 38 (179/472) | Chlorobium tepidum FusA/NodT (475 aa) family of multidrug-resistant proteins (AAM72516.1). Contains To1C and OEP and outer membrane and efflux motifs. |
| 15937-13490 | orf11 | 815 | 46 (378/821) | Chlorobium tepidum AcrB/AcrD (1,063 aa) family of multidrug-resistant proteins (AAM72517.1). Has the motif of the AcrB/AcrD/AcrF family of proteins associated with antibiotic resistance due to efflux pumps. |
| 17127-16101 | orf12 | 373 | 34 (128/367) | Chlorobium tepidum AcrA/AcrE (396 aa) family of multidrug-resistant proteins (AAM72518.1). Has a motif contained by AcrA, HlyD, and EmrA families of proteins involved with membrane fusion, secretion, and multidrug resistance efflux. |
| 18373-17171 | orf13 | 400 | N terminus, 32 (59/182); C terminus, 33 (55/164) | N-terminal end B. subtilis TagO (358 aa) tcichoic acid linkage unit synthesis (B69721). C-terminal of end acetyltransferase (GNAT) family YnaD (170 aa) B. subtilis (AAB41084.1). Contains motifs for two families of proteins: Rfe, UDP-N-acetylmuramyl pentapeptide phosphotransferase, and RimL, acetyltransferases. |