Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 107504 |
| Name | oriT_R69  |
| Organism | Salmonella enterica subsp. enterica serovar Paratyphi B strain R69 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_KM406488 (35543..35646 [-], 104 nt) |
| oriT length | 104 nt |
| IRs (inverted repeats) | 31..36, 39..44 (GCCGGC..GCCGGC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 104 nt
>oriT_R69
AGTACGGGACAAGATGTGTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
AGTACGGGACAAGATGTGTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 5028 | GenBank | WP_004206924 |
| Name | Relaxase_HTD90_RS00180_R69 |
UniProt ID | A0A2V4FJ40 |
| Length | 659 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 659 a.a. Molecular weight: 75087.84 Da Isoelectric Point: 10.0285
>WP_004206924.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFAGIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQLRSESDDKFNPK
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFAGIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQLRSESDDKFNPK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A2V4FJ40 |
T4CP
| ID | 5238 | GenBank | WP_004206885 |
| Name | t4cp2_HTD90_RS00435_R69 |
UniProt ID | _ |
| Length | 695 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 695 a.a. Molecular weight: 79538.91 Da Isoelectric Point: 4.8317
>WP_004206885.1 MULTISPECIES: conjugal transfer protein TrbC [Enterobacterales]
MQQESVDSKKVLRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMRFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM
MQQESVDSKKVLRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMRFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 13550..32745
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTD90_RS00065 | 11238..12305 | - | 1068 | WP_024190316 | plasmid replication initiator RepA | - |
| HTD90_RS00070 | 12590..12820 | - | 231 | WP_004187496 | IncL/M type plasmid replication protein RepC | - |
| HTD90_RS00075 | 12894..13547 | - | 654 | WP_004206935 | hypothetical protein | - |
| HTD90_RS00080 | 13550..15730 | - | 2181 | WP_004187492 | DotA/TraY family protein | traY |
| HTD90_RS00085 | 15723..16373 | - | 651 | WP_004187488 | hypothetical protein | - |
| HTD90_RS00090 | 16370..17578 | - | 1209 | WP_004187486 | conjugal transfer protein TraW | traW |
| HTD90_RS00095 | 17575..20625 | - | 3051 | WP_011154474 | conjugative transfer protein | traU |
| HTD90_RS00100 | 20723..21115 | - | 393 | WP_227626115 | hypothetical protein | - |
| HTD90_RS00105 | 21161..21550 | - | 390 | WP_011154472 | DUF6750 family protein | traR |
| HTD90_RS00110 | 21567..22097 | - | 531 | WP_172686291 | conjugal transfer protein TraQ | traQ |
| HTD90_RS00115 | 22121..22825 | - | 705 | WP_004206933 | conjugal transfer protein TraP | traP |
| HTD90_RS00120 | 22837..24186 | - | 1350 | WP_004206932 | conjugal transfer protein TraO | traO |
| HTD90_RS00125 | 24198..25349 | - | 1152 | WP_015062843 | DotH/IcmK family type IV secretion protein | traN |
| HTD90_RS00130 | 25358..26140 | - | 783 | WP_004206929 | DotI/IcmL family type IV secretion protein | traM |
| HTD90_RS00135 | 26139..26549 | + | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| HTD90_RS00140 | 26536..26733 | + | 198 | WP_004187464 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| HTD90_RS00145 | 26734..27288 | - | 555 | WP_011154467 | hypothetical protein | traL |
| HTD90_RS00525 | 27313..28275 | - | 963 | WP_227991741 | hypothetical protein | - |
| HTD90_RS00530 | 28340..28759 | - | 420 | WP_346009424 | LPD7 domain-containing protein | - |
| HTD90_RS00535 | 28696..28893 | - | 198 | WP_227991742 | hypothetical protein | - |
| HTD90_RS00155 | 28890..30518 | - | 1629 | WP_172686292 | toprim domain-containing protein | - |
| HTD90_RS00160 | 30543..30802 | - | 260 | Protein_34 | IcmT/TraK family protein | - |
| HTD90_RS00165 | 30792..31955 | - | 1164 | WP_004206926 | plasmid transfer ATPase TraJ | virB11 |
| HTD90_RS00170 | 31966..32745 | - | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| HTD90_RS00175 | 32742..33242 | - | 501 | WP_004206925 | DotD/TraH family lipoprotein | - |
| HTD90_RS00180 | 33256..35235 | - | 1980 | WP_004206924 | TraI/MobA(P) family conjugative relaxase | - |
| HTD90_RS00185 | 35222..35539 | - | 318 | WP_004206923 | plasmid mobilization protein MobA | - |
| HTD90_RS00190 | 35814..36218 | + | 405 | WP_227991743 | MobC | - |
| HTD90_RS00195 | 36679..37215 | - | 537 | WP_004206920 | hypothetical protein | - |
| HTD90_RS00200 | 37348..37659 | - | 312 | WP_004187333 | hypothetical protein | - |
Host bacterium
| ID | 7939 | GenBank | NZ_KM406488 |
| Plasmid name | R69 | Incompatibility group | IncL/M |
| Plasmid size | 78899 bp | Coordinate of oriT [Strand] | 35543..35646 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Paratyphi B strain R69 |
Cargo genes
| Drug resistance gene | blaTEM-1D, aph(3')-Ia, tet(B) |
| Virulence gene | - |
| Metal resistance gene | merE, merD, merA, merC, merP, merT, merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIIA8 |