Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100746 |
| Name | oriT_p12-4374_96  |
| Organism | Salmonella enterica subsp. enterica serovar Heidelberg strain 12-4374 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP012929 (42721..42830 [-], 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_p12-4374_96
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 818 | GenBank | WP_001474686 |
| Name | NikB_p12-4374_96 |
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
>WP_001474686.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
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: 48190..85935
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| APS45_RS24100 (APS45_23400) | 45906..48197 | - | 2292 | WP_001289271 | F-type conjugative transfer protein TrbC | - |
| APS45_RS24105 (APS45_23405) | 48190..49260 | - | 1071 | WP_000151575 | IncI1-type conjugal transfer protein TrbB | trbB |
| APS45_RS24110 (APS45_23410) | 49279..50487 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| APS45_RS24115 (APS45_23415) | 50779..50931 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| APS45_RS24120 (APS45_23420) | 51003..51254 | - | 252 | WP_001291965 | hypothetical protein | - |
| APS45_RS27030 | 52178..52354 | - | 177 | WP_001054900 | hypothetical protein | - |
| APS45_RS24125 (APS45_23425) | 52746..52955 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| APS45_RS24130 (APS45_23430) | 53027..53689 | - | 663 | WP_000644794 | plasmid IncI1-type surface exclusion protein ExcA | - |
| APS45_RS24135 (APS45_23435) | 53760..55928 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| APS45_RS24140 (APS45_23440) | 56025..56609 | - | 585 | WP_001037998 | conjugal transfer protein TraX | - |
| APS45_RS24145 (APS45_23445) | 56638..57840 | - | 1203 | WP_001189158 | IncI1-type conjugal transfer protein TraW | traW |
| APS45_RS25970 | 57807..58421 | - | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| APS45_RS24150 (APS45_23450) | 58421..61465 | - | 3045 | WP_001024752 | IncI1-type conjugal transfer protein TraU | traU |
| APS45_RS24155 (APS45_23455) | 61555..62355 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| APS45_RS24160 (APS45_23460) | 62339..62527 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| APS45_RS24165 (APS45_23465) | 62591..62995 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| APS45_RS24170 (APS45_23470) | 63046..63573 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| APS45_RS24175 (APS45_23475) | 63573..64277 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| APS45_RS24180 (APS45_23480) | 64277..65566 | - | 1290 | WP_001271997 | conjugal transfer protein TraO | traO |
| APS45_RS24185 (APS45_23485) | 65569..66552 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| APS45_RS24190 (APS45_23490) | 66563..67255 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| APS45_RS24195 (APS45_23495) | 67252..67599 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| APS45_RS24200 (APS45_23500) | 67617..71384 | - | 3768 | WP_001141535 | LPD7 domain-containing protein | - |
| APS45_RS24205 (APS45_23505) | 71474..72025 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| APS45_RS25975 | 72040..72330 | - | 291 | WP_001299214 | hypothetical protein | traK |
| APS45_RS24210 (APS45_23510) | 72327..73475 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| APS45_RS24215 (APS45_23515) | 73472..74290 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| APS45_RS24220 (APS45_23520) | 74287..74745 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| APS45_RS24225 (APS45_23525) | 75140..75724 | - | 585 | WP_000977517 | histidine phosphatase family protein | - |
| APS45_RS24230 (APS45_23530) | 75784..76986 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| APS45_RS24235 (APS45_23535) | 77072..77896 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| APS45_RS24240 (APS45_23540) | 78047..79201 | - | 1155 | WP_001139958 | site-specific integrase | - |
| APS45_RS27490 | 79787..80008 | + | 222 | Protein_87 | prepilin | - |
| APS45_RS24255 (APS45_23555) | 80005..81429 | - | 1425 | WP_023278060 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| APS45_RS25985 | 81429..82085 | - | 657 | WP_001193553 | prepilin peptidase | - |
| APS45_RS24260 (APS45_23560) | 82070..82630 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| APS45_RS24265 (APS45_23565) | 82640..83254 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| APS45_RS24270 (APS45_23570) | 83272..84369 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| APS45_RS24275 (APS45_23575) | 84382..85935 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| APS45_RS24280 (APS45_23580) | 85946..86398 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| APS45_RS24285 (APS45_23585) | 86385..87680 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| APS45_RS24290 (APS45_23590) | 87673..89355 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| APS45_RS24295 (APS45_23595) | 89369..89806 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| APS45_RS25990 | 89806..90873 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 1206 | GenBank | NZ_CP012929 |
| Plasmid name | p12-4374_96 | Incompatibility group | IncI1 |
| Plasmid size | 96042 bp | Coordinate of oriT [Strand] | 42721..42830 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Heidelberg strain 12-4374 |
Cargo genes
| Drug resistance gene | blaCMY-2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |