Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 107505 |
| Name | oriT_pSEM  |
| Organism | Salmonella enterica subsp. enterica serovar Typhimurium strain 202 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_KM406490 (28731..28836 [-], 106 nt) |
| oriT length | 106 nt |
| IRs (inverted repeats) | 30..35, 41..46 (CCGCCG..CGGCGG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 106 nt
>oriT_pSEM
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 5029 | GenBank | WP_059509498 |
| Name | Relaxase_HTD53_RS00125_pSEM |
UniProt ID | A0A0E3MRA0 |
| Length | 659 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 659 a.a. Molecular weight: 75193.92 Da Isoelectric Point: 9.9948
>WP_059509498.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQIFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQIFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A0E3MRA0 |
T4CP
| ID | 5239 | GenBank | WP_004187443 |
| Name | t4cp2_HTD53_RS00010_pSEM |
UniProt ID | _ |
| Length | 695 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 695 a.a. Molecular weight: 79519.87 Da Isoelectric Point: 4.8309
>WP_004187443.1 MULTISPECIES: hypothetical protein [Enterobacterales]
MQQESVDSKKVIRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMHFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM
MQQESVDSKKVIRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMHFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 6741..25935
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTD53_RS00565 | 3108..3203 | - | 96 | WP_004206884 | DinQ-like type I toxin DqlB | - |
| HTD53_RS00015 | 4058..4300 | - | 243 | WP_172686030 | hypothetical protein | - |
| HTD53_RS00020 | 4430..5497 | - | 1068 | WP_019725043 | plasmid replication initiator RepA | - |
| HTD53_RS00560 | 5865..6011 | - | 147 | WP_346341332 | IncL/M type plasmid replication protein RepC | - |
| HTD53_RS00025 | 6085..6738 | - | 654 | WP_004206935 | hypothetical protein | - |
| HTD53_RS00030 | 6741..8921 | - | 2181 | WP_004187492 | DotA/TraY family protein | traY |
| HTD53_RS00035 | 8914..9564 | - | 651 | WP_004187488 | hypothetical protein | - |
| HTD53_RS00040 | 9561..10769 | - | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| HTD53_RS00045 | 10766..13816 | - | 3051 | WP_031942490 | plasmid transfer protein | traU |
| HTD53_RS00050 | 13813..14307 | - | 495 | WP_011091080 | hypothetical protein | - |
| HTD53_RS00055 | 14353..14742 | - | 390 | WP_011091078 | DUF6750 family protein | traR |
| HTD53_RS00060 | 14759..15289 | - | 531 | WP_011091077 | conjugal transfer protein TraQ | traQ |
| HTD53_RS00065 | 15313..16017 | - | 705 | WP_031942491 | conjugal transfer protein TraP | traP |
| HTD53_RS00070 | 16029..17378 | - | 1350 | WP_011091075 | conjugal transfer protein TraO | traO |
| HTD53_RS00075 | 17390..18541 | - | 1152 | WP_011091074 | DotH/IcmK family type IV secretion protein | traN |
| HTD53_RS00080 | 18550..19332 | - | 783 | WP_011091073 | DotI/IcmL family type IV secretion protein | traM |
| HTD53_RS00085 | 19331..19741 | + | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| HTD53_RS00090 | 19728..19925 | + | 198 | WP_004187464 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| HTD53_RS00095 | 19926..20438 | - | 513 | WP_011091071 | hypothetical protein | traL |
| HTD53_RS00535 | 20404..21468 | - | 1065 | WP_227992071 | hypothetical protein | - |
| HTD53_RS00540 | 21569..23707 | - | 2139 | WP_227992073 | LPD7 domain-containing protein | - |
| HTD53_RS00105 | 23732..23992 | - | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| HTD53_RS00110 | 23982..25145 | - | 1164 | WP_004187313 | plasmid transfer ATPase TraJ | virB11 |
| HTD53_RS00115 | 25156..25935 | - | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| HTD53_RS00120 | 25932..26432 | - | 501 | WP_004187320 | DotD/TraH family lipoprotein | - |
| HTD53_RS00125 | 26446..28425 | - | 1980 | WP_059509498 | TraI/MobA(P) family conjugative relaxase | - |
| HTD53_RS00545 | 28412..28975 | - | 564 | WP_227992076 | plasmid mobilization protein MobA | - |
| HTD53_RS00135 | 28974..29369 | + | 396 | WP_172686305 | MobC | - |
| HTD53_RS00140 | 29870..30406 | - | 537 | WP_011091066 | hypothetical protein | - |
| HTD53_RS00145 | 30539..30850 | - | 312 | WP_004187333 | hypothetical protein | - |
Host bacterium
| ID | 7940 | GenBank | NZ_KM406490 |
| Plasmid name | pSEM | Incompatibility group | IncL/M |
| Plasmid size | 79502 bp | Coordinate of oriT [Strand] | 28731..28836 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Typhimurium strain 202 |
Cargo genes
| Drug resistance gene | tet(A), sul1, qacE, ant(3'')-Ia, aac(3)-Ia, blaSHV-5 |
| Virulence gene | - |
| Metal resistance gene | merR, merT, merP, merC, merA, merD, merE |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIIA8 |