TABLE 1.
CDSs of the vanA plasmids pVEF1 and pVEF2
| CDS no. | CDSa | Nucleotide position (5′→3′)
|
Protein length (aac) | Database match (accession no.) | aa identity (%) | Alignment region of the match | |
|---|---|---|---|---|---|---|---|
| pVEF1 | pVEF2b | ||||||
| 1 | rep | 1-1500 | = | 499 | Plasmid replication protein in E. faecium DO (ZP_00602529) | 99 | 1-499/499 |
| 2 | prgN | 1636-1923 | = | 95 | pRUM prgN, E. faecium (Q848V1) | 57 | 1-96/96 |
| 3 | TIS1216 | 2427-2089 | = | 112 | IS1216 on pRE25, pRUM, pTEF1, pTEF3, pUW786, and pE418 (e.g., CAC29206) | 98 | 117-228/228 |
| 4 | HcP | 2946-3116 | = | 56 | pRE25 orf7, hypothetical conserved protein (CAC29163) | 100 | 1-56/56 |
| 5 | resIP | 3130-3747 | = | 205 | pGB354 resolvase, Streptococcus agalactiae (AAB48454) | 100 | 1-205/205 |
| 6 | top beta | 3747-5891 | = | 714 | pAMbeta1 type 1 topoisomerase E. faecalis (AAC38606) | 97 | 1-714/714 |
| 7 | δ | 5994-6890 | = | 298 | pIlo8 delta protein, Oenococcus oeni (CAD70616)/pSM19035 active partitioning δ protein (YP_232765) | 100/98 | 1-298/298 |
| 8 | ω | 6982-7197 | = | 71 | pRE25 orf17 (CAC29172)/pSM19035 transcriptional repressor ω (YP_232757) | 100/100 | 1-71/71 |
| 9 | Ttransposase | 7272-7802 | = | 176 | pLI100 transposase, Listeria innocua (CAC42047) | 98 | 51-226/226 |
| 10 | Tstr | 8084-8647 | = | 188 | N-terminal part of pS194 streptomycin resistance protein, S. aureus (P12055) | 95 | 1-188/282 |
| 11 | vanZ | 9383-8898 | = | 161 | pIP816 vanZ (Q06242) | 100 | 1-161/161 |
| 12 | vanY | 10447-9536 | = | 303 | pIP816 vanY (P37711) | 100 | 1-303/303 |
| 13 | vanX | 11483-10875 | = | 202 | pIP816 vanX (AAA65957) | 100 | 1-202/202 |
| 14 | vanA | 12520-11489 | = | 343 | pIP816 vanA (P25051) | 100 | 1-343/343 |
| 15 | vanH | 13481-12513 | = | 322 | pIP816 vanH (Q05709) | 100 | 1-322/322 |
| 16 | vanS | 14850-13696 | = | 384 | pIP816 vanS (Q06240) | 100 | 1-384/384 |
| 17 | vanR | 15523-14828 | = | 231 | pIP816 vanR (Q06239) | 100 | 1-231/231 |
| 18 | resTn1546 | 16312-15737 | = | 191 | pIP816 resolvase (Q06237) | 100 | 1-191/191 |
| 19 | Tn1546 transposase | 16458-19424 | = | 988 | pIP816 Tn1546 transposase (Q06238) | 100 | 1-988/988 |
| 20 | Tstr | 19504-19788 | = | 94 | C-terminal part of pS194 streptomycin resistance protein, S. aureus (P12055) | 95 | 189-282/282 |
| 21 | Ttransposase | 20102-20443 | = | 114 | pLI100 pLI0020 protein, putative transposase of L. innocua (Q926N5) | 87 | 1-114/160 |
| 22 | Ttransposase | 20430-20786 | = | 118 | pLI100 pLI0071 protein, putative transposase of L. innocua (Q925W6) | 85 | 117-224/226 |
| 23 | IS1216 | 21506-20820 | 21594-20908 | 228 | IS1216 on pRE25, pRUM, pTEF1, pTEF3, pUW786, and pE418 (e.g., CAC29206) | 100 | 1-228/228 |
| 24 | prgO | 21951-21676 | 22039-21764 | 91 | pRE25 prgO (CAC29214) | 100 | 1-91/91 |
| 25 | prgP | 22876-21923 | 22964-22011 | 317 | pRE25 prgP (CAC29215) | 100 | 1-317/317 |
| 26 | repR | 23488-24981 | 23576-25069 | 497 | pRE25 repR, orf1 (Q9AL28) | 100 | 1-497/497 |
| 27 | prgN | 25023-25412 | 25204-25500 | 98 | pRE25 prgN (Q9AL27) | 100 | 1-98/98 |
| 28 | HcP | 25513-26364 | 25601-26452 | 283 | Hypothetical conserved protein of E. faecium DO (EAN10371)/pRE25 hypothetical protein orf4 (Q9AL25) | 100/99 | 1-283/283 |
| 29 | IS1216 | 27024-27710 | 27112-27798 | 228 | IS1216, E. faecium (Q9KI43)/IS1216 on pRE25, pRUM, pTEF1, pTEF3, pUW786, pUW1965, and pE418 (e.g., CAC29206) | 100/99 | 1-228/228 |
| 30 | Tδ | 27752-27940 | 27840-28028 | 62 | pIlo1 delta protein, O. oeni (CAD70608) | 91 | 238-298/298 |
| 31 | ω | 28032-28247 | 28120-28335 | 71 | pRE25 orf17 (CAC29172)/pSM19035 transcriptional repressor ω (YP_232757) | 100/100 | 1-71/71 |
| 32 | ε | 28265-28537 | 28353-28625 | 90 | pRE25 orf18 epsilon antitoxin 2 (Q9AL19)/pSM19035 ɛ antitoxin (Q57231) | 100/78 | 1-90/90 |
| 33 | ξ | 28539-29402 | 28627-29490 | 287 | pRE25 orf19 ζ toxin (P0A4M1)/pSM19035 ζ toxin (Q54944) | 100/91 | 1-287/287 |
| 34 | THcP | 29524-29823 | 29579-29911 | 99 | pRE25 orf21 hypothetical conserved protein (CAC29176) | 97 | 1-99/168 |
| 35 | Transcriptional regulator | 30702-30106 | 30790-30194 | 198 | Regulatory protein, TetR-family, E. faecium DO (ZP_00602897) | 67 | 1-195/195 |
| 36 | ABC transporter | 31014-31895 | 31102-31983 | 293 | ABC transporter ATP-binding protein Oceanobacillus iheyensis (Q8ESC1) | 83 | 1-293/293 |
| 37 | HcP | 31919-33532 | 32007-33620 | 537 | Hypothetical conserved protein, O. iheyensis (Q8ESC0) | 71 | 1-537/537 |
| 38 | HP | 34194-33604 | 34282-33692 | 196 | Hypothetical protein | ||
| 39 | IS256 | 34341-35531 | 34429-35619 | 396 | Transposase, IS256 family, E. faecalis V583 (AA081627) | 95 | 1-396/396 |
| 40 | rec/int | 36026-36625 | 36114-36713 | 199 | pE88 recombinase/integrase, Clostridium tetani (AAO37444) | 40 | 1-190:1-192/202d |
| 41 | IS1216 | 37535-36849 | 37623-36937 | 228 | IS1216 on pRE25, pRUM, pTEF1, pTEF3, pUW786, and pE418 (e.g., CAC29206) | 100 | 1-228/228 |
| 42 | HP | 38163-37792 | 38251-37880 | 123 | Hypothetical protein | ||
| 43 | ATPase | 39076-38165 | 39164-38253 | 303 | pX02 ATPase, ParA family, CapR protein, Bacillus anthracis (NP_653010) | 53 | 19-300:4-283/288d |
a
T, truncated CDS; HcP, hypothetical conserved protein; HP, hypothetical protein.
b
=, identical to the nucleotide positions in pVEF1.
c
aa, amino acids.
d
Query alignment region:match alignment region/total aa of the match.