Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100459 |
| Name | oriT_pNF1358  |
| Organism | Salmonella enterica |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019099 (43525..43634 [-], 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_pNF1358
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 530 | GenBank | YP_006954608 |
| Name | Relaxase_pNF1358 |
UniProt ID | Q4FIJ3 |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103977.42 Da Isoelectric Point: 7.2753
>YP_006954608.1 relaxase (plasmid) [Salmonella enterica]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYIAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYIAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q4FIJ3 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 48994..89269
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HS380_RS00290 | 46710..49001 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HS380_RS00295 | 48994..50064 | - | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| HS380_RS00300 | 50083..51291 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HS380_RS00305 (D645_p2028) | 51583..51735 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| HS380_RS00310 | 51807..52058 | - | 252 | WP_001291965 | hypothetical protein | - |
| HS380_RS00315 | 52101..52265 | + | 165 | WP_001323923 | hypothetical protein | - |
| HS380_RS00320 | 52424..53206 | - | 783 | WP_001317493 | IS21-like element IS100kyp family helper ATPase IstB | - |
| HS380_RS00325 | 53203..54225 | - | 1023 | WP_000255944 | IS21-like element IS100 family transposase | - |
| HS380_RS00335 | 55011..55295 | - | 285 | WP_014640317 | hypothetical protein | - |
| HS380_RS00340 | 55579..55788 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HS380_RS00345 (D645_p2030) | 55860..56522 | - | 663 | WP_000644794 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HS380_RS00350 (D645_p2031) | 56593..58761 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| HS380_RS00355 (D645_p2032) | 58858..59442 | - | 585 | WP_001037998 | conjugal transfer protein TraX | - |
| HS380_RS00360 (D645_p2033) | 59471..60673 | - | 1203 | WP_001697941 | IncI1-type conjugal transfer protein TraW | traW |
| HS380_RS00365 (D645_p2034) | 60640..61254 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| HS380_RS00370 (D645_p2035) | 61254..64298 | - | 3045 | WP_010891269 | IncI1-type conjugal transfer protein TraU | traU |
| HS380_RS00375 (D645_p2036) | 64388..65188 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HS380_RS00380 (D645_p2037) | 65172..65360 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HS380_RS00385 (D645_p2038) | 65424..65828 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| HS380_RS00390 | 65879..66406 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HS380_RS00395 (D645_p2039) | 66406..67110 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HS380_RS00400 (D645_p2040) | 67110..68399 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| HS380_RS00405 (D645_p2041) | 68402..69385 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| HS380_RS00410 (D645_p2042) | 69396..70088 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| HS380_RS00415 (D645_p2043) | 70085..70432 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HS380_RS00420 (D645_p2044) | 70450..74217 | - | 3768 | WP_010891270 | LPD7 domain-containing protein | - |
| HS380_RS00425 (D645_p2046) | 74307..74858 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| HS380_RS00430 (D645_p2047) | 74873..75163 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HS380_RS00435 (D645_p2048) | 75160..76308 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HS380_RS00440 (D645_p2049) | 76305..77123 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HS380_RS00445 (D645_p2050) | 77120..77578 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HS380_RS00450 (D645_p2051) | 77973..78557 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HS380_RS00455 (D645_p2052) | 78617..79819 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| HS380_RS00460 (D645_p2053) | 79905..80729 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| HS380_RS00465 (D645_p2054) | 80880..82034 | - | 1155 | WP_001139958 | site-specific integrase | - |
| HS380_RS00470 | 82018..82344 | + | 327 | WP_001213803 | hypothetical protein | - |
| HS380_RS00475 | 82695..82850 | + | 156 | WP_001302705 | hypothetical protein | - |
| HS380_RS00580 | 83118..83342 | + | 225 | Protein_94 | hypothetical protein | - |
| HS380_RS00485 (D645_p2055) | 83339..84763 | - | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HS380_RS00490 (D645_p2056) | 84763..85419 | - | 657 | WP_001389386 | prepilin peptidase | - |
| HS380_RS00495 (D645_p2057) | 85404..85964 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HS380_RS00500 (D645_p2058) | 85974..86588 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| HS380_RS00505 (D645_p2059) | 86606..87703 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| HS380_RS00510 (D645_p2060) | 87716..89269 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HS380_RS00515 (D645_p2061) | 89280..89732 | - | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| HS380_RS00520 (D645_p2062) | 89719..91014 | - | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
| HS380_RS00525 (D645_p2063) | 91007..92689 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HS380_RS00530 (D645_p2064) | 92703..93140 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HS380_RS00535 (D645_p2065) | 93140..94207 | - | 1068 | WP_001302629 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 920 | GenBank | NC_019099 |
| Plasmid name | pNF1358 | Incompatibility group | IncI1 |
| Plasmid size | 99331 bp | Coordinate of oriT [Strand] | 43525..43634 [-] |
| Host baterium | Salmonella enterica |
Cargo genes
| Drug resistance gene | blaCMY-5 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |