Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100090 |
| Name | oriT_pGO1  |
| Organism | Staphylococcus aureus |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NC_012547 (10191..10226 [+], 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 | _ |
oriT sequence
Download Length: 36 nt
>oriT_pGO1
CACGCGAACGGAACGTTCGCATAAGTGCGCCCTTAC
CACGCGAACGGAACGTTCGCATAAGTGCGCCCTTAC
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Climo MW et al. (1996) Identification and characterization of the origin of conjugative transfer (oriT) and a gene (nes) encoding a single-stranded endonuclease on the Staphylococcal plasmid pGO1. J Bacteriol. 178(16):4975-83. [PMID:8759863]
Relaxase
| ID | 85 | GenBank | YP_002790904 |
| Name | Nes_pGO1  |
UniProt ID | O87361 |
| Length | 665 a.a. | PDB ID | |
| Note | oriT relaxase Nes | ||
Relaxase protein sequence
Download Length: 665 a.a. Molecular weight: 78908.86 Da Isoelectric Point: 5.3910
>YP_002790904.1 oriT relaxase Nes (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 |
Reference
[1] Climo MW et al. (1996) Identification and characterization of the origin of conjugative transfer (oriT) and a gene (nes) encoding a single-stranded endonuclease on the Staphylococcal plasmid pGO1. J Bacteriol. 178(16):4975-83. [PMID:8759863]
T4CP
| ID | 85 | GenBank | YP_002790929 |
| Name | TrsK_pGO1 |
UniProt ID | Q07713 |
| Length | 546 a.a. | PDB ID | _ |
| Note | similar to transfer-associated proteins of Gram-negative conjugation systems such as TraD from the F plasmid | ||
T4CP protein sequence
Download Length: 546 a.a. Molecular weight: 62672.60 Da Isoelectric Point: 7.6569
>YP_002790929.1 TrsK protein (plasmid) [Staphylococcus aureus]
MTTLLGELESKATSINKKNLVIQDFDTKCPNRNIFVVGGPGSYKSAGYVIPNVIVKNQQSIVVTDPSGEV
YEKTSNIKRMQGFDVRVVNFKNFLASDRQNFFDYIDKDSDCSIVAELIIKSAGDSKINKDVWYKASVGLL
NSLLLYAKYEFEPEKRTIGNIIKFIQNNKPNQDEEGSVELDKRFNELSKDHPARESYEFGFAVSEGRTRA
SIILTFVADLRNYIDNEIRSYTSDSDFDLRDVGLRKTIIYVMLPVLGNTVQSLSSLFFSQMFQQLYRLGD
ENGARLPVPVDFLLDEWPNIGAIPDYEETLATCRKYGISITTIVQSISQAVDKYNKDKANAIIGNHAVIL
CLGNVNNDTAKYIKEELGNATVEFETSSEGSSSGKDSRSKSSNKNVSYTGRALLNEDEISNMQQDKAILI
TKNRNPKIIKKLAYFKMFPNLTETYIAPQNEYKRKKNQSMIDKHNRLREEWDKKQEKNKQQKLEEYKEEQ
RQKELEKEQQPQEEQQNEKVKESKDKNDQEDKKDEQQKINDSKKAFYEKLKQKQAK
MTTLLGELESKATSINKKNLVIQDFDTKCPNRNIFVVGGPGSYKSAGYVIPNVIVKNQQSIVVTDPSGEV
YEKTSNIKRMQGFDVRVVNFKNFLASDRQNFFDYIDKDSDCSIVAELIIKSAGDSKINKDVWYKASVGLL
NSLLLYAKYEFEPEKRTIGNIIKFIQNNKPNQDEEGSVELDKRFNELSKDHPARESYEFGFAVSEGRTRA
SIILTFVADLRNYIDNEIRSYTSDSDFDLRDVGLRKTIIYVMLPVLGNTVQSLSSLFFSQMFQQLYRLGD
ENGARLPVPVDFLLDEWPNIGAIPDYEETLATCRKYGISITTIVQSISQAVDKYNKDKANAIIGNHAVIL
CLGNVNNDTAKYIKEELGNATVEFETSSEGSSSGKDSRSKSSNKNVSYTGRALLNEDEISNMQQDKAILI
TKNRNPKIIKKLAYFKMFPNLTETYIAPQNEYKRKKNQSMIDKHNRLREEWDKKQEKNKQQKLEEYKEEQ
RQKELEKEQQPQEEQQNEKVKESKDKNDQEDKKDEQQKINDSKKAFYEKLKQKQAK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q07713 |
Reference
[1] Gomis-Rüth FX et al. (2002) Conjugative plasmid protein TrwB, an integral membrane type IV secretion system coupling protein. Detailed structural features and mapping of the active site cleft. J Biol Chem. 277(9):7556-66. [PMID:11748238]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 25492..36713
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PGO1_RS00115 (PGO1_p20) | 21240..21644 | - | 405 | WP_001242578 | bleomycin binding protein | - |
| PGO1_RS00120 (PGO1_p21) | 21861..22631 | - | 771 | WP_001795128 | aminoglycoside O-nucleotidyltransferase ANT(4')-Ia | - |
| PGO1_RS00125 | 22791..22937 | - | 147 | WP_001817822 | hypothetical protein | - |
| PGO1_RS00130 (PGO1_p22) | 22981..23655 | + | 675 | WP_001106019 | IS6-like element IS257 family transposase | - |
| PGO1_RS00135 (PGO1_p23) | 23764..23952 | - | 189 | WP_001063224 | hypothetical protein | - |
| PGO1_RS00140 (PGO1_p24) | 24124..25098 | + | 975 | WP_000368849 | conjugative transfer protein TrsA | - |
| PGO1_RS00145 (PGO1_p25) | 25115..25432 | + | 318 | WP_000591622 | CagC family type IV secretion system protein | - |
| PGO1_RS00150 (PGO1_p26) | 25492..25899 | + | 408 | WP_000110157 | hypothetical protein | trsC |
| PGO1_RS00155 (PGO1_p27) | 25886..26569 | + | 684 | WP_000979860 | TrsD/TraD family conjugative transfer protein | trsD |
| PGO1_RS00160 (PGO1_p28) | 26584..28602 | + | 2019 | WP_001795400 | DUF87 domain-containing protein | virb4 |
| PGO1_RS00165 (PGO1_p29) | 28614..29894 | + | 1281 | WP_000702361 | membrane protein | trsF |
| PGO1_RS00170 (PGO1_p30) | 29912..30988 | + | 1077 | WP_000269385 | CHAP domain-containing protein | trsG |
| PGO1_RS00175 (PGO1_p31) | 30998..31483 | + | 486 | WP_000735569 | TrsH/TraH family protein | - |
| PGO1_RS00180 (PGO1_p32) | 31499..33601 | + | 2103 | WP_001094109 | DNA topoisomerase III | - |
| PGO1_RS00185 (PGO1_p33) | 33617..34081 | + | 465 | WP_000715273 | hypothetical protein | trsJ |
| PGO1_RS00190 (PGO1_p34) | 34078..35718 | + | 1641 | WP_000209436 | VirD4-like conjugal transfer protein, CD1115 family | - |
| PGO1_RS00195 (PGO1_p35) | 35796..36713 | + | 918 | WP_000383804 | conjugal transfer protein TrbL family protein | trsL |
| PGO1_RS00200 (PGO1_p36) | 36730..37122 | + | 393 | WP_000608970 | single-stranded DNA-binding protein | - |
| PGO1_RS00205 (PGO1_p37) | 37179..37346 | + | 168 | WP_000869301 | hypothetical protein | - |
| PGO1_RS00210 (PGO1_p38) | 37384..38058 | + | 675 | WP_001105984 | IS6-like element IS257 family transposase | - |
| PGO1_RS00215 (PGO1_p39) | 38162..39085 | + | 924 | WP_001579520 | protein rep | - |
| PGO1_RS00220 (PGO1_p40) | 39618..39839 | - | 222 | WP_000799767 | hypothetical protein | - |
| PGO1_RS00225 (PGO1_p41) | 40057..40380 | - | 324 | WP_001146389 | quaternary ammonium compound efflux SMR transporter QacC | - |
| PGO1_RS00230 | 40688..40918 | + | 231 | WP_000956386 | hypothetical protein | - |
| PGO1_RS00235 (PGO1_p42) | 40948..41622 | + | 675 | WP_001105984 | IS6-like element IS257 family transposase | - |
Host bacterium
| ID | 85 | GenBank | NC_012547 |
| Plasmid name | pGO1 | Incompatibility group | Inc18 |
| Plasmid size | 54000 bp | Coordinate of oriT [Strand] | 10191..10226 [+] |
| Host baterium | Staphylococcus aureus |
Cargo genes
| Drug resistance gene | aminoglycoside resistance; resistance to trimethoprim,bleomycin and quaternary ammonium compounds |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIIA21 |