Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100243 |
| Name | oriT_pLW043  |
| Organism | Staphylococcus aureus |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NC_005054 (54976..55011 [+], 36 nt) |
| oriT length | 36 nt |
| IRs (inverted repeats) | 4..10, 14..20 (GCGAACG..CGTTCGC) |
| Location of nic site | 31..32 |
| Conserved sequence flanking the nic site |
TAAGTGCGCC|CT |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 36 nt
>oriT_pLW043
CACGCGAACGGAACGTTCGCATAAGTGCGCCCTTAC
CACGCGAACGGAACGTTCGCATAAGTGCGCCCTTAC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 314 | GenBank | NP_878032 |
| Name | nickingenzyme_pLW043 |
UniProt ID | O87361 |
| Length | 665 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 665 a.a. Molecular weight: 78908.86 Da Isoelectric Point: 5.3910
>NP_878032.1 nicking enzyme (plasmid) [Staphylococcus aureus]
MAMYHFQNKFVSKANGQSATAKSAYNSASRIKDFKENEFKDYSNKQCDYSEILLPNNADDKFKDREYLWN
KVHDVENRKNSQVAREIIIGLPNEFDPNSNIELAKEFAESLSNEGMIVDLNIHKINEENPHAHLLCTLRG
LDKNNEFEPKRKGNDYIRDWNTKEKHNEWRKRWENVQNKHLEKNGFSVRVSADSYKNQNIDLEPTKKEGW
KARKFEDETGKKSSISKHNESIKKRNQQKIDKMFNEVDDMKSHKLNAFSYMNKSDSTTLKNMAKDLKIYV
TPINMYKENERLYDLKQKTSLITDDEDRLNKIEDIEDRQKKLESINEVFEKQAGIFFDKNYPDQSLNYSD
DEKIFITRTILNDRDVLPANNELEDIVKEKRIKEAQISLNTVLGNRDISLESIEKESNFFADKLSNILEK
NNLSFDDVLENKHEGMEDSLKIDYYTNKLEVFRNAENILEDYYDVQIKELFTDDEDYKAFNEVTDIKEKQ
QLIDFKTYHGTENTIEMLETGNFIPKYSDEDRKYITEQVKLLQEKEFKPNKNQHDKFVFGAIQKKLLSEY
DFDYSDNNDLKHLYQESNEVGDEISKDNIEEFYEGNDILVDKETYNNYNRKQQAYGLINAGLDSMIFNFN
EIFRERMPKYINHQYKGKNHSKQRHELKNKRGMHL
MAMYHFQNKFVSKANGQSATAKSAYNSASRIKDFKENEFKDYSNKQCDYSEILLPNNADDKFKDREYLWN
KVHDVENRKNSQVAREIIIGLPNEFDPNSNIELAKEFAESLSNEGMIVDLNIHKINEENPHAHLLCTLRG
LDKNNEFEPKRKGNDYIRDWNTKEKHNEWRKRWENVQNKHLEKNGFSVRVSADSYKNQNIDLEPTKKEGW
KARKFEDETGKKSSISKHNESIKKRNQQKIDKMFNEVDDMKSHKLNAFSYMNKSDSTTLKNMAKDLKIYV
TPINMYKENERLYDLKQKTSLITDDEDRLNKIEDIEDRQKKLESINEVFEKQAGIFFDKNYPDQSLNYSD
DEKIFITRTILNDRDVLPANNELEDIVKEKRIKEAQISLNTVLGNRDISLESIEKESNFFADKLSNILEK
NNLSFDDVLENKHEGMEDSLKIDYYTNKLEVFRNAENILEDYYDVQIKELFTDDEDYKAFNEVTDIKEKQ
QLIDFKTYHGTENTIEMLETGNFIPKYSDEDRKYITEQVKLLQEKEFKPNKNQHDKFVFGAIQKKLLSEY
DFDYSDNNDLKHLYQESNEVGDEISKDNIEEFYEGNDILVDKETYNNYNRKQQAYGLINAGLDSMIFNFN
EIFRERMPKYINHQYKGKNHSKQRHELKNKRGMHL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| PDB | 4HTE | |
| AlphaFold DB | O87361 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 6425..17646
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| VRA_RS00015 (VRA0003) | 1909..2307 | - | 399 | Protein_2 | DegV family protein | - |
| VRA_RS00020 (VRA0004) | 2317..2802 | - | 486 | WP_000175735 | trimethoprim-resistant dihydrofolate reductase DfrS1 | - |
| VRA_RS00025 (VRA0005) | 2844..3800 | - | 957 | WP_000282655 | thymidylate synthase | - |
| VRA_RS00030 (VRA0006) | 3914..4588 | + | 675 | WP_001106019 | IS6-like element IS257 family transposase | - |
| VRA_RS00035 (VRA0007) | 4697..4885 | - | 189 | WP_001063224 | hypothetical protein | - |
| VRA_RS00040 (VRA0008) | 5057..6031 | + | 975 | WP_000368849 | conjugative transfer protein TrsA | - |
| VRA_RS00045 (VRA0009) | 6048..6365 | + | 318 | WP_000591622 | CagC family type IV secretion system protein | - |
| VRA_RS00050 (VRA0010) | 6425..6832 | + | 408 | WP_000110157 | hypothetical protein | trsC |
| VRA_RS00055 (VRA0011) | 6819..7502 | + | 684 | WP_000979860 | TrsD/TraD family conjugative transfer protein | trsD |
| VRA_RS00060 (VRA0012) | 7517..9535 | + | 2019 | WP_001795400 | DUF87 domain-containing protein | virb4 |
| VRA_RS00065 (VRA0013) | 9547..10827 | + | 1281 | WP_000702363 | membrane protein | trsF |
| VRA_RS00070 (VRA0014) | 10845..11921 | + | 1077 | WP_000269385 | CHAP domain-containing protein | trsG |
| VRA_RS00075 (VRA0015) | 11931..12416 | + | 486 | WP_000735569 | TrsH/TraH family protein | - |
| VRA_RS00080 (VRA0016) | 12432..14534 | + | 2103 | WP_001094109 | DNA topoisomerase III | - |
| VRA_RS00085 (VRA0017) | 14550..15014 | + | 465 | WP_000715273 | hypothetical protein | trsJ |
| VRA_RS00090 (VRA0018) | 15011..16651 | + | 1641 | WP_000209436 | VirD4-like conjugal transfer protein, CD1115 family | - |
| VRA_RS00095 (VRA0019) | 16729..17646 | + | 918 | WP_000383804 | conjugal transfer protein TrbL family protein | trsL |
| VRA_RS00100 (VRA0020) | 17663..18055 | + | 393 | WP_000608970 | single-stranded DNA-binding protein | - |
| VRA_RS00105 (VRA0021) | 18112..18279 | + | 168 | WP_000869301 | hypothetical protein | - |
| VRA_RS00110 (VRA0022) | 18317..18991 | + | 675 | WP_001105984 | IS6-like element IS257 family transposase | - |
| VRA_RS00115 (VRA0023) | 19095..20018 | + | 924 | WP_001579520 | protein rep | - |
| VRA_RS00120 (VRA0025) | 20551..20772 | - | 222 | WP_000799767 | hypothetical protein | - |
| VRA_RS00125 (VRA0026) | 20990..21313 | - | 324 | WP_001146389 | quaternary ammonium compound efflux SMR transporter QacC | - |
| VRA_RS00130 | 21621..21851 | + | 231 | WP_000956386 | hypothetical protein | - |
| VRA_RS00135 (VRA0027) | 21881..22555 | + | 675 | WP_001105984 | IS6-like element IS257 family transposase | - |
Host bacterium
| ID | 705 | GenBank | NC_005054 |
| Plasmid name | pLW043 | Incompatibility group | _ |
| Plasmid size | 57889 bp | Coordinate of oriT [Strand] | 54976..55011 [+] |
| Host baterium | Staphylococcus aureus |
Cargo genes
| Drug resistance gene | qacD, aac(6')-aph(2''), VanHAX, blaZ |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIIA21 |