Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100471 |
| Name | oriT_pSH1148_107  |
| Organism | Salmonella enterica subsp. enterica serovar Heidelberg |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019123 (53782..53884 [-], 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_pSH1148_107
TCAGCTCCTTACTGGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTCAGG
TCAGCTCCTTACTGGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 542 | GenBank | YP_006957265 |
| Name | Relaxase_pSH1148_107 |
UniProt ID | H9TKJ4 |
| 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
>YP_006957265.1 relaxase/ mobilization nucelase domain (plasmid) [Salmonella enterica subsp. enterica serovar Heidelberg]
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
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | H9TKJ4 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 59250..96726
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS928_RS00320 (pSH1148_107_78) | 56966..59257 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HS928_RS00325 (pSH1148_107_79) | 59250..60320 | - | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| HS928_RS00330 (pSH1148_107_80) | 60339..61547 | - | 1209 | WP_000121274 | IncI1-type conjugal transfer protein TrbA | trbA |
| HS928_RS00335 (pSH1148_107_81) | 61839..61991 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| HS928_RS00580 (pSH1148_107_82) | 62063..62254 | - | 192 | WP_174715448 | hypothetical protein | - |
| HS928_RS00585 | 62815..62910 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| HS928_RS00345 | 62975..63259 | - | 285 | WP_172684476 | hypothetical protein | - |
| HS928_RS00350 (pSH1148_107_86) | 63543..63752 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HS928_RS00355 (pSH1148_107_87) | 63824..64486 | - | 663 | WP_000653334 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HS928_RS00360 (pSH1148_107_88) | 64551..66713 | - | 2163 | WP_000698351 | DotA/TraY family protein | traY |
| HS928_RS00365 (pSH1148_107_89) | 66810..67394 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| HS928_RS00370 (pSH1148_107_90) | 67423..68625 | - | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| HS928_RS00375 (pSH1148_107_91) | 68592..69206 | - | 615 | WP_000337398 | IncI1-type conjugal transfer protein TraV | traV |
| HS928_RS00380 (pSH1148_107_92) | 69206..72250 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| HS928_RS00385 (pSH1148_107_93) | 72340..73140 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HS928_RS00390 (pSH1148_107_94) | 73124..73312 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HS928_RS00395 (pSH1148_107_95) | 73376..73780 | - | 405 | WP_000086957 | IncI1-type conjugal transfer protein TraR | traR |
| HS928_RS00400 (pSH1148_107_96) | 73831..74358 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HS928_RS00405 (pSH1148_107_97) | 74358..75062 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HS928_RS00410 (pSH1148_107_98) | 75062..76351 | - | 1290 | WP_001272005 | conjugal transfer protein TraO | traO |
| HS928_RS00415 (pSH1148_107_99) | 76354..77337 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| HS928_RS00420 (pSH1148_107_100) | 77348..78040 | - | 693 | WP_000138548 | DotI/IcmL family type IV secretion protein | traM |
| HS928_RS00425 (pSH1148_107_101) | 78037..78384 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HS928_RS00430 (pSH1148_107_102) | 78402..82169 | - | 3768 | WP_001141529 | LPD7 domain-containing protein | - |
| HS928_RS00435 (pSH1148_107_103) | 82259..82810 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| HS928_RS00440 (pSH1148_107_104) | 82825..83115 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HS928_RS00445 (pSH1148_107_105) | 83112..84260 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HS928_RS00450 (pSH1148_107_106) | 84257..85075 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HS928_RS00455 (pSH1148_107_107) | 85072..85530 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HS928_RS00460 (pSH1148_107_108) | 85925..86509 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HS928_RS00465 (pSH1148_107_109) | 86569..87771 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| HS928_RS00470 (pSH1148_107_110) | 87856..88680 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| HS928_RS00475 (pSH1148_107_111) | 88831..89985 | - | 1155 | WP_001139957 | site-specific integrase | - |
| HS928_RS00480 | 89969..90295 | + | 327 | WP_001213803 | hypothetical protein | - |
| HS928_RS00485 (pSH1148_107_113) | 90922..92220 | - | 1299 | Protein_98 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HS928_RS00490 (pSH1148_107_114) | 92220..92876 | - | 657 | WP_001193553 | prepilin peptidase | - |
| HS928_RS00495 (pSH1148_107_115) | 92861..93421 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HS928_RS00500 (pSH1148_107_116) | 93431..94045 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| HS928_RS00505 (pSH1148_107_117) | 94063..95160 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| HS928_RS00510 (pSH1148_107_118) | 95173..96726 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HS928_RS00515 (pSH1148_107_119) | 96737..97189 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| HS928_RS00520 (pSH1148_107_120) | 97176..98471 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| HS928_RS00525 (pSH1148_107_121) | 98464..100146 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HS928_RS00530 (pSH1148_107_122) | 100160..100597 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HS928_RS00535 (pSH1148_107_123) | 100597..101664 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 932 | GenBank | NC_019123 |
| Plasmid name | pSH1148_107 | Incompatibility group | IncI1 |
| Plasmid size | 106833 bp | Coordinate of oriT [Strand] | 53782..53884 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Heidelberg |
Cargo genes
| Drug resistance gene | sul1, qacE, aac(3)-VIa, ant(3'')-Ia |
| Virulence gene | htpB |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |