Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100649 |
| Name | oriT_pCVM22462  |
| Organism | Salmonella enterica subsp. enterica serovar Newport str. CVM 22462 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP009566 (75953..76062 [+], 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_pCVM22462
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 721 | GenBank | WP_010891268 |
| Name | Relaxase_pCVM22462 |
UniProt ID | _ |
| 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
>WP_010891268.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
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
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 32295..70593
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SEEN462_RS00180 (SEEN462_00210) | 27357..28424 | + | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
| SEEN462_RS00185 (SEEN462_00215) | 28424..28861 | + | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| SEEN462_RS00190 (SEEN462_00220) | 28875..30557 | + | 1683 | WP_032311054 | PilN family type IVB pilus formation outer membrane protein | - |
| SEEN462_RS00195 (SEEN462_00225) | 30550..31845 | + | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| SEEN462_RS00200 (SEEN462_00230) | 31832..32284 | + | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| SEEN462_RS00205 (SEEN462_00235) | 32295..33848 | + | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| SEEN462_RS00210 (SEEN462_00240) | 33861..34958 | + | 1098 | WP_001208805 | type II secretion system F family protein | - |
| SEEN462_RS00215 (SEEN462_00245) | 34976..35590 | + | 615 | WP_044436008 | type 4 pilus major pilin | - |
| SEEN462_RS00220 (SEEN462_00250) | 35600..36160 | + | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| SEEN462_RS25385 | 36145..36801 | + | 657 | WP_001193553 | prepilin peptidase | - |
| SEEN462_RS00225 (SEEN462_00255) | 36801..38092 | + | 1292 | Protein_47 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| SEEN462_RS27490 (SEEN462_00260) | 38089..38337 | - | 249 | WP_001349157 | hypothetical protein | - |
| SEEN462_RS00235 (SEEN462_00285) | 39857..41011 | + | 1155 | WP_001139957 | site-specific integrase | - |
| SEEN462_RS00240 (SEEN462_00290) | 41162..41986 | + | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| SEEN462_RS00245 (SEEN462_00295) | 42071..43273 | + | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| SEEN462_RS00250 (SEEN462_00300) | 43333..43917 | + | 585 | WP_000977522 | histidine phosphatase family protein | - |
| SEEN462_RS00255 (SEEN462_00305) | 44312..44770 | + | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| SEEN462_RS00260 (SEEN462_00310) | 44767..45585 | + | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| SEEN462_RS00265 (SEEN462_00315) | 45582..46730 | + | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| SEEN462_RS25415 (SEEN462_00320) | 46727..47017 | + | 291 | WP_001299214 | hypothetical protein | traK |
| SEEN462_RS00270 (SEEN462_00325) | 47032..47583 | + | 552 | WP_000014583 | phospholipase D family protein | - |
| SEEN462_RS00275 (SEEN462_00330) | 47673..51440 | + | 3768 | WP_001141527 | LPD7 domain-containing protein | - |
| SEEN462_RS00280 (SEEN462_00335) | 51458..51805 | + | 348 | WP_001055900 | conjugal transfer protein | traL |
| SEEN462_RS00285 (SEEN462_00340) | 51802..52494 | + | 693 | WP_000138550 | DotI/IcmL family type IV secretion protein | traM |
| SEEN462_RS00290 (SEEN462_00345) | 52505..53488 | + | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| SEEN462_RS00295 (SEEN462_00350) | 53491..54780 | + | 1290 | WP_001272003 | conjugal transfer protein TraO | traO |
| SEEN462_RS00300 (SEEN462_00355) | 54780..55484 | + | 705 | WP_000801919 | IncI1-type conjugal transfer protein TraP | traP |
| SEEN462_RS00305 (SEEN462_00360) | 55484..56011 | + | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| SEEN462_RS00310 (SEEN462_00365) | 56062..56466 | + | 405 | WP_000086959 | IncI1-type conjugal transfer protein TraR | traR |
| SEEN462_RS00315 (SEEN462_00370) | 56530..56718 | + | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| SEEN462_RS00320 (SEEN462_00375) | 56702..57502 | + | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| SEEN462_RS00325 (SEEN462_00380) | 57592..60636 | + | 3045 | WP_001024782 | IncI1-type conjugal transfer protein TraU | traU |
| SEEN462_RS00330 (SEEN462_00385) | 60636..61250 | + | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| SEEN462_RS00335 (SEEN462_00390) | 61217..62419 | + | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| SEEN462_RS00340 (SEEN462_00395) | 62448..63032 | + | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| SEEN462_RS00345 (SEEN462_00400) | 63129..65297 | + | 2169 | WP_000698357 | DotA/TraY family protein | traY |
| SEEN462_RS00350 (SEEN462_00405) | 65371..66021 | + | 651 | WP_001178506 | plasmid IncI1-type surface exclusion protein ExcA | - |
| SEEN462_RS00355 (SEEN462_00410) | 66093..66302 | - | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| SEEN462_RS28030 | 66694..66870 | + | 177 | WP_001054897 | hypothetical protein | - |
| SEEN462_RS28455 (SEEN462_00420) | 66935..67030 | - | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| SEEN462_RS00365 (SEEN462_00430) | 67529..67780 | + | 252 | WP_001291964 | hypothetical protein | - |
| SEEN462_RS00370 (SEEN462_00435) | 67852..68004 | - | 153 | WP_001331364 | Hok/Gef family protein | - |
| SEEN462_RS00375 (SEEN462_00440) | 68296..69504 | + | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| SEEN462_RS00380 (SEEN462_00445) | 69523..70593 | + | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| SEEN462_RS00385 (SEEN462_00450) | 70586..72877 | + | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
Host bacterium
| ID | 1109 | GenBank | NZ_CP009566 |
| Plasmid name | pCVM22462 | Incompatibility group | IncI1 |
| Plasmid size | 94725 bp | Coordinate of oriT [Strand] | 75953..76062 [+] |
| Host baterium | Salmonella enterica subsp. enterica serovar Newport str. CVM 22462 |
Cargo genes
| Drug resistance gene | resistance to cetylpyridinium; quaternary ammonium compound-resistance |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |