Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100757 |
| Name | oriT_PDM04  |
| Organism | Salmonella enterica subsp. enterica serovar Anatum strain GT-38 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP013224 (75907..76009 [-], 103 nt) |
| oriT length | 103 nt |
| IRs (inverted repeats) | IR1: 19..26, 30..37 (GTCGGGGC..GCCCTGAC) IR2: 44..58, 67..81 (GCAATTGTATAATCG..CGGTTATACAATTGC) |
| Location of nic site | 89..90 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 103 nt
>oriT_PDM04
TCAGCTCCTTACTGGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTCAGG
TCAGCTCCTTACTGGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 829 | GenBank | WP_001354015 |
| Name | NikB_PDM04 |
UniProt ID | _ |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104018.47 Da Isoelectric Point: 7.3526
>WP_001354015.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCLAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCLAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 81375..110805
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| AS586_RS00425 (AS586_23815) | 79091..81382 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| AS586_RS00430 (AS586_23820) | 81375..82445 | - | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| AS586_RS00435 (AS586_23825) | 82464..83672 | - | 1209 | WP_000121274 | IncI1-type conjugal transfer protein TrbA | trbA |
| AS586_RS00440 (AS586_23830) | 83964..84116 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| AS586_RS27075 | 84188..84379 | - | 192 | WP_174715448 | hypothetical protein | - |
| AS586_RS27080 | 84940..85035 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| AS586_RS26630 | 85100..85276 | - | 177 | WP_001054904 | hypothetical protein | - |
| AS586_RS00450 (AS586_23840) | 85668..85877 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| AS586_RS00455 (AS586_23845) | 85949..86611 | - | 663 | WP_000653334 | plasmid IncI1-type surface exclusion protein ExcA | - |
| AS586_RS00460 (AS586_23850) | 86676..88838 | - | 2163 | WP_000698351 | DotA/TraY family protein | traY |
| AS586_RS00465 (AS586_23855) | 88935..89519 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| AS586_RS00470 (AS586_23860) | 89548..90750 | - | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| AS586_RS24205 | 90717..91331 | - | 615 | WP_000337398 | IncI1-type conjugal transfer protein TraV | traV |
| AS586_RS00475 (AS586_23865) | 91331..94375 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| AS586_RS00480 (AS586_23870) | 94465..95265 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| AS586_RS00485 (AS586_23875) | 95249..95437 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| AS586_RS00490 (AS586_23880) | 95501..95905 | - | 405 | WP_000086957 | IncI1-type conjugal transfer protein TraR | traR |
| AS586_RS00495 (AS586_23885) | 95956..96483 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| AS586_RS00500 (AS586_23890) | 96483..97187 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| AS586_RS00505 (AS586_23895) | 97187..98476 | - | 1290 | WP_001272005 | conjugal transfer protein TraO | traO |
| AS586_RS00510 (AS586_23900) | 98479..99462 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| AS586_RS00515 (AS586_23905) | 99473..100165 | - | 693 | WP_000138548 | DotI/IcmL family type IV secretion protein | traM |
| AS586_RS00520 (AS586_23910) | 100162..100509 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| AS586_RS00525 (AS586_23915) | 100527..104294 | - | 3768 | WP_001141529 | LPD7 domain-containing protein | - |
| AS586_RS00530 (AS586_23920) | 104384..104935 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| AS586_RS24210 | 104950..105240 | - | 291 | WP_001299214 | hypothetical protein | traK |
| AS586_RS00535 (AS586_23925) | 105237..106385 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| AS586_RS00540 (AS586_23930) | 106382..107200 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| AS586_RS00545 (AS586_23935) | 107197..107655 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| AS586_RS00550 (AS586_23940) | 108050..108634 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| AS586_RS00555 (AS586_23945) | 108694..109896 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| AS586_RS00560 (AS586_23950) | 109981..110805 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| AS586_RS00565 (AS586_23955) | 110956..112110 | - | 1155 | WP_001139957 | site-specific integrase | - |
Host bacterium
| ID | 1217 | GenBank | NZ_CP013224 |
| Plasmid name | PDM04 | Incompatibility group | IncI1 |
| Plasmid size | 112176 bp | Coordinate of oriT [Strand] | 75907..76009 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Anatum strain GT-38 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |