Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100465 |
| Name | oriT_pSal8934a  |
| Organism | Salmonella enterica subsp. enterica serovar Typhimurium |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019111 (55295..55404 [+], 110 nt) |
| oriT length | 110 nt |
| IRs (inverted repeats) | IR1: 24..31, 35..42 (GTCGGGGC..GCCCTGAC) IR2: 49..65, 72..88 (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC) |
| 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_pSal8934a
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 536 | GenBank | YP_006955719 |
| Name | TrbD_pSal8934a |
UniProt ID | Q79VV7 |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104010.41 Da Isoelectric Point: 7.4265
>YP_006955719.1 TrbD (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q79VV7 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 11559..49935
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS913_RS00045 (pSal8934a012) | 6621..7688 | + | 1068 | WP_001302629 | type IV pilus biogenesis lipoprotein PilL | - |
| HS913_RS00050 (pSal8934a013) | 7688..8125 | + | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HS913_RS00055 (pSal8934a014) | 8139..9821 | + | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HS913_RS00060 (pSal8934a015) | 9814..11109 | + | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
| HS913_RS00065 (pSal8934a016) | 11096..11548 | + | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| HS913_RS00070 (pSal8934a017) | 11559..13112 | + | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HS913_RS00075 (pSal8934a018) | 13125..14222 | + | 1098 | WP_001208805 | type II secretion system F family protein | - |
| HS913_RS00080 (pSal8934a019) | 14240..14854 | + | 615 | WP_000959786 | type 4 pilus major pilin | - |
| HS913_RS00085 (pSal8934a020) | 14864..15424 | + | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HS913_RS00090 (pSal8934a021) | 15409..16065 | + | 657 | WP_001193553 | prepilin peptidase | - |
| HS913_RS00095 (pSal8934a022) | 16065..17489 | + | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HS913_RS00555 | 17486..17707 | - | 222 | Protein_20 | prepilin | - |
| HS913_RS00540 (pSal8934a025) | 18161..18550 | + | 390 | WP_223873413 | shufflon protein D' | - |
| HS913_RS00545 | 18839..19138 | - | 300 | WP_223873359 | pilus assembly protein PilV | - |
| HS913_RS00115 (pSal8934a026) | 19122..20276 | + | 1155 | WP_001139958 | site-specific integrase | - |
| HS913_RS00120 (pSal8934a027) | 20427..21251 | + | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| HS913_RS00125 (pSal8934a028) | 21337..22539 | + | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| HS913_RS00130 (pSal8934a029) | 22599..23183 | + | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HS913_RS00135 (pSal8934a031) | 23578..24036 | + | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HS913_RS00140 (pSal8934a032) | 24033..24851 | + | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HS913_RS00145 (pSal8934a033) | 24848..25996 | + | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HS913_RS00150 (pSal8934a034) | 25993..26283 | + | 291 | WP_001299214 | hypothetical protein | traK |
| HS913_RS00155 (pSal8934a035) | 26298..26849 | + | 552 | WP_000014584 | phospholipase D family protein | - |
| HS913_RS00160 (pSal8934a036) | 26939..30708 | + | 3770 | Protein_32 | LPD7 domain-containing protein | - |
| HS913_RS00165 (pSal8934a039) | 30726..31073 | + | 348 | WP_001055900 | conjugal transfer protein | traL |
| HS913_RS00170 (pSal8934a040) | 31070..31762 | + | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| HS913_RS00175 (pSal8934a041) | 31773..32756 | + | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| HS913_RS00180 (pSal8934a042) | 32759..34048 | + | 1290 | WP_001271997 | conjugal transfer protein TraO | traO |
| HS913_RS00185 (pSal8934a043) | 34048..34752 | + | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HS913_RS00190 (pSal8934a044) | 34752..35279 | + | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HS913_RS00195 (pSal8934a045) | 35330..35734 | + | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| HS913_RS00200 (pSal8934a046) | 35798..35986 | + | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HS913_RS00205 (pSal8934a047) | 35970..36770 | + | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HS913_RS00210 (pSal8934a048) | 36860..39904 | + | 3045 | WP_001024752 | IncI1-type conjugal transfer protein TraU | traU |
| HS913_RS00215 (pSal8934a050) | 39904..40518 | + | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| HS913_RS00220 (pSal8934a051) | 40485..41687 | + | 1203 | WP_015059431 | IncI1-type conjugal transfer protein TraW | traW |
| HS913_RS00225 (pSal8934a052) | 41716..42300 | + | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| HS913_RS00230 (pSal8934a053) | 42397..44565 | + | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| HS913_RS00235 (pSal8934a054) | 44641..45255 | + | 615 | WP_000578649 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HS913_RS00240 (pSal8934a055) | 45353..45562 | + | 210 | WP_001140545 | hemolysin expression modulator Hha | - |
| HS913_RS00245 (pSal8934a056) | 45663..45947 | + | 285 | WP_014640317 | hypothetical protein | - |
| HS913_RS00250 | 46664..46828 | - | 165 | WP_001323923 | hypothetical protein | - |
| HS913_RS00255 | 46871..47122 | + | 252 | WP_001291965 | hypothetical protein | - |
| HS913_RS00260 (pSal8934a059) | 47194..47346 | - | 153 | WP_001303307 | Hok/Gef family protein | - |
| HS913_RS00265 (pSal8934a060) | 47638..48846 | + | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HS913_RS00270 (pSal8934a061) | 48865..49935 | + | 1071 | WP_000151582 | IncI1-type conjugal transfer protein TrbB | trbB |
| HS913_RS00275 (pSal8934a062) | 49928..52219 | + | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
Host bacterium
| ID | 926 | GenBank | NC_019111 |
| Plasmid name | pSal8934a | Incompatibility group | IncI1 |
| Plasmid size | 91369 bp | Coordinate of oriT [Strand] | 55295..55404 [+] |
| Host baterium | Salmonella enterica subsp. enterica serovar Typhimurium |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |