Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 107525 |
| Name | oriT_R471  |
| Organism | Serratia marcescens strain R471 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_KM406489 (85447..85551 [-], 105 nt) |
| oriT length | 105 nt |
| IRs (inverted repeats) | 32..37, 40..45 (GCCGGC..GCCGGC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 105 nt
>oriT_R471
AGTACGGGACAAGATGTGTTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
AGTACGGGACAAGATGTGTTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 5051 | GenBank | WP_015062826 |
| Name | Relaxase_HTD98_RS00530_R471 |
UniProt ID | I3W4P9 |
| Length | 659 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 659 a.a. Molecular weight: 75186.91 Da Isoelectric Point: 9.9948
>WP_015062826.1 TraI/MobA(P) family conjugative relaxase [Serratia marcescens]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLIRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQNTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSIDERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLIRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQNTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSIDERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | I3W4P9 |
T4CP
| ID | 5271 | GenBank | WP_004187443 |
| Name | t4cp2_HTD98_RS00260_R471 |
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: 63539..82647
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTD98_RS00395 | 58692..59117 | - | 426 | WP_000522996 | organomercurial transporter MerC | - |
| HTD98_RS00400 | 59145..59420 | - | 276 | WP_000732275 | mercury resistance system periplasmic binding protein MerP | - |
| HTD98_RS00405 | 59436..59801 | - | 366 | WP_001294656 | mercuric ion transporter MerT | - |
| HTD98_RS00410 | 59873..60328 | + | 456 | WP_001166628 | Hg(II)-responsive transcriptional regulator | - |
| HTD98_RS00415 | 61219..62286 | - | 1068 | WP_172686394 | plasmid replication initiator RepA | - |
| HTD98_RS00420 | 62572..62820 | - | 249 | WP_015062836 | IncL/M type plasmid replication protein RepC | - |
| HTD98_RS00425 | 62884..63537 | - | 654 | WP_015062835 | hypothetical protein | - |
| HTD98_RS00430 | 63539..65734 | - | 2196 | WP_015062834 | DotA/TraY family protein | traY |
| HTD98_RS00435 | 65727..66323 | - | 597 | WP_015060003 | hypothetical protein | - |
| HTD98_RS00440 | 66320..67528 | - | 1209 | WP_004187486 | conjugal transfer protein TraW | traW |
| HTD98_RS00445 | 67525..70575 | - | 3051 | WP_015062833 | IncI1 plasmid conjugative transfer protein TraU | traU |
| HTD98_RS00450 | 70673..71065 | - | 393 | WP_227626115 | hypothetical protein | - |
| HTD98_RS00455 | 71111..71500 | - | 390 | WP_015062832 | DUF6750 family protein | traR |
| HTD98_RS00460 | 71517..72047 | - | 531 | WP_011091077 | conjugal transfer protein TraQ | traQ |
| HTD98_RS00465 | 72071..72775 | - | 705 | WP_015062831 | conjugal transfer protein TraP | traP |
| HTD98_RS00470 | 72787..74136 | - | 1350 | WP_015062830 | conjugal transfer protein TraO | traO |
| HTD98_RS00475 | 74148..75299 | - | 1152 | WP_011091074 | DotH/IcmK family type IV secretion protein | traN |
| HTD98_RS00480 | 75308..76090 | - | 783 | WP_015062829 | DotI/IcmL family type IV secretion protein | traM |
| HTD98_RS00485 | 76089..76499 | + | 411 | WP_004187465 | H-NS family nucleoid-associated regulatory protein | - |
| HTD98_RS00490 | 76486..76683 | + | 198 | WP_004187464 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| HTD98_RS00495 | 76684..77196 | - | 513 | WP_011091071 | hypothetical protein | traL |
| HTD98_RS00550 | 77162..78226 | - | 1065 | WP_227991876 | hypothetical protein | - |
| HTD98_RS00555 | 78327..78707 | - | 381 | WP_346341331 | LPD7 domain-containing protein | - |
| HTD98_RS00560 | 78644..79051 | - | 408 | WP_227991879 | hypothetical protein | - |
| HTD98_RS00505 | 79056..80420 | - | 1365 | WP_172686395 | toprim domain-containing protein | - |
| HTD98_RS00510 | 80445..80704 | - | 260 | Protein_105 | IcmT/TraK family protein | - |
| HTD98_RS00515 | 80694..81857 | - | 1164 | WP_015062827 | plasmid transfer ATPase TraJ | virB11 |
| HTD98_RS00520 | 81868..82647 | - | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| HTD98_RS00525 | 82644..83146 | - | 503 | Protein_108 | DotD/TraH family lipoprotein | - |
| HTD98_RS00530 | 83160..85139 | - | 1980 | WP_015062826 | TraI/MobA(P) family conjugative relaxase | - |
| HTD98_RS00535 | 85126..85443 | - | 318 | WP_004206923 | plasmid mobilization protein MobA | - |
| HTD98_RS00540 | 85689..86015 | + | 327 | WP_227991880 | MobC | - |
Host bacterium
| ID | 7960 | GenBank | NZ_KM406489 |
| Plasmid name | R471 | Incompatibility group | IncL/M |
| Plasmid size | 86748 bp | Coordinate of oriT [Strand] | 85447..85551 [-] |
| Host baterium | Serratia marcescens strain R471 |
Cargo genes
| Drug resistance gene | blaTEM-1B |
| Virulence gene | - |
| Metal resistance gene | merR2, merB, merD, merE, merA, merC, merP, merT, merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIIA8 |