Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100611 |
| Name | oriT_pJIE512b  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_025198 (38515..38624 [-], 110 nt) |
| oriT length | 110 nt |
| IRs (inverted repeats) | IR1: 24..31, 35..42 (GTCGGGGC..GCCCTGAC) IR2: 49..65, 72..88 (GTAATTGTAATAGCGTC..GACGGTATTACAATTAC) |
| Location of nic site | 96..97 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 110 nt
>oriT_pJIE512b
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 683 | GenBank | YP_009072152 |
| Name | NikB_pJIE512b |
UniProt ID | _ |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103834.33 Da Isoelectric Point: 7.3473
>YP_009072152.1 relaxase protein NikB (plasmid) [Escherichia coli]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 43984..82232
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| H4J97_RS00280 (D616_p157067) | 41700..43991 | - | 2292 | WP_072107381 | F-type conjugative transfer protein TrbC | - |
| H4J97_RS00285 (D616_p157068) | 43984..45054 | - | 1071 | WP_000151576 | IncI1-type conjugal transfer protein TrbB | trbB |
| H4J97_RS00290 (D616_p157069) | 45073..46281 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| H4J97_RS00295 (D616_p157071) | 46573..46725 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| H4J97_RS00300 (D616_p157072) | 46797..47048 | - | 252 | WP_001291967 | hypothetical protein | - |
| H4J97_RS00565 | 47547..47642 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| H4J97_RS00305 (D616_p157074) | 47707..48051 | - | 345 | WP_181394993 | hypothetical protein | - |
| H4J97_RS00310 (D616_p157075) | 48226..48435 | + | 210 | WP_000062602 | HEAT repeat domain-containing protein | - |
| H4J97_RS00315 (D616_p157076) | 48507..49169 | - | 663 | WP_032073207 | plasmid IncI1-type surface exclusion protein ExcA | - |
| H4J97_RS00320 (D616_p157077) | 49234..51396 | - | 2163 | WP_000698351 | DotA/TraY family protein | traY |
| H4J97_RS00325 (D616_p157078) | 51493..52077 | - | 585 | WP_001037985 | IncI1-type conjugal transfer protein TraX | - |
| H4J97_RS00330 (D616_p157079) | 52106..53308 | - | 1203 | WP_021555368 | IncI1-type conjugal transfer protein TraW | traW |
| H4J97_RS00335 (D616_p157080) | 53275..53889 | - | 615 | WP_001542516 | IncI1-type conjugal transfer protein TraV | traV |
| H4J97_RS00340 (D616_p157081) | 53889..56933 | - | 3045 | WP_001024779 | IncI1-type conjugal transfer protein TraU | traU |
| H4J97_RS00345 (D616_p157082) | 57023..57823 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| H4J97_RS00350 (D616_p157083) | 57807..57995 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| H4J97_RS00355 (D616_p157084) | 58059..58463 | - | 405 | WP_000086957 | IncI1-type conjugal transfer protein TraR | traR |
| H4J97_RS00360 (D616_p157085) | 58514..59041 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| H4J97_RS00365 (D616_p157086) | 59041..59745 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| H4J97_RS00370 (D616_p157087) | 59745..61034 | - | 1290 | WP_001272005 | conjugal transfer protein TraO | traO |
| H4J97_RS00375 (D616_p157088) | 61037..62020 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| H4J97_RS00380 (D616_p157089) | 62031..62723 | - | 693 | WP_000138548 | DotI/IcmL family type IV secretion protein | traM |
| H4J97_RS00385 (D616_p157090) | 62720..63067 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| H4J97_RS00390 (D616_p157091) | 63085..66852 | - | 3768 | WP_032073208 | LPD7 domain-containing protein | - |
| H4J97_RS00395 | 66942..67493 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| H4J97_RS00400 | 67508..67798 | - | 291 | WP_001299214 | hypothetical protein | traK |
| H4J97_RS00405 (D616_p157093) | 67795..68943 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| H4J97_RS00410 (D616_p157094) | 68940..69758 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| H4J97_RS00415 (D616_p157095) | 69755..70213 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| H4J97_RS00420 (D616_p157096) | 70608..71192 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| H4J97_RS00425 (D616_p157097) | 71252..72454 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| H4J97_RS00430 (D616_p157098) | 72539..73363 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| H4J97_RS00435 (D616_p157099) | 73514..74668 | - | 1155 | WP_001139957 | site-specific integrase | - |
| H4J97_RS00440 | 74652..74984 | + | 333 | WP_094190803 | shufflon protein C | - |
| H4J97_RS00445 | 74981..75136 | - | 156 | WP_001302705 | hypothetical protein | - |
| H4J97_RS00450 | 75797..76054 | + | 258 | WP_001302706 | hypothetical protein | - |
| H4J97_RS00455 | 76189..76437 | + | 249 | WP_001349157 | hypothetical protein | - |
| H4J97_RS00460 (D616_p157100) | 76434..77726 | - | 1293 | WP_001417545 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| H4J97_RS00465 (D616_p157101) | 77726..78382 | - | 657 | WP_001193553 | prepilin peptidase | - |
| H4J97_RS00470 (D616_p157102) | 78367..78927 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| H4J97_RS00475 (D616_p157103) | 78937..79551 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| H4J97_RS00480 (D616_p157104) | 79569..80666 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| H4J97_RS00485 (D616_p157105) | 80679..82232 | - | 1554 | WP_032073210 | ATPase, T2SS/T4P/T4SS family | virB11 |
| H4J97_RS00490 (D616_p157106) | 82243..82695 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| H4J97_RS00495 (D616_p157107) | 82682..83977 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| H4J97_RS00500 (D616_p157108) | 83970..85652 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| H4J97_RS00505 (D616_p157109) | 85666..86103 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| H4J97_RS00510 (D616_p157110) | 86103..87170 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 1071 | GenBank | NC_025198 |
| Plasmid name | pJIE512b | Incompatibility group | IncI1 |
| Plasmid size | 92339 bp | Coordinate of oriT [Strand] | 38515..38624 [-] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | blaCMY-2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |