Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100300 |
| Name | oriT_pCVM29188_101  |
| Organism | Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_011077 (43719..43828 [-], 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_pCVM29188_101
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 371 | GenBank | WP_001474686 |
| Name | NikB_pCVM29188_101 |
UniProt ID | B4TL30 |
| 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: 49188..88892
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SEKA_RS29280 (SeKA_C0079) | 46904..49195 | - | 2292 | WP_001289271 | F-type conjugative transfer protein TrbC | - |
| SEKA_RS29285 (SeKA_C0080) | 49188..50258 | - | 1071 | WP_000151575 | IncI1-type conjugal transfer protein TrbB | trbB |
| SEKA_RS29290 (SeKA_C0081) | 50277..51485 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| SEKA_RS29295 (SeKA_C0082) | 51777..51929 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| SEKA_RS29300 (SeKA_C0083) | 52001..52252 | - | 252 | WP_001291965 | hypothetical protein | - |
| SEKA_RS29305 (SeKA_C0086) | 52613..53395 | - | 783 | WP_001300609 | IS21-like element IS100kyp family helper ATPase IstB | - |
| SEKA_RS29310 (SeKA_C0087) | 53392..54414 | - | 1023 | WP_001572805 | IS21-like element IS100 family transposase | - |
| SEKA_RS33590 (SeKA_C0089) | 55135..55311 | - | 177 | WP_001054900 | hypothetical protein | - |
| SEKA_RS29315 (SeKA_C0091) | 55703..55912 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| SEKA_RS29320 (SeKA_C0092) | 55984..56646 | - | 663 | WP_000644794 | plasmid IncI1-type surface exclusion protein ExcA | - |
| SEKA_RS29325 (SeKA_C0093) | 56717..58885 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| SEKA_RS29330 (SeKA_C0094) | 58982..59566 | - | 585 | WP_001037998 | conjugal transfer protein TraX | - |
| SEKA_RS29335 (SeKA_C0095) | 59595..60797 | - | 1203 | WP_001189158 | IncI1-type conjugal transfer protein TraW | traW |
| SEKA_RS31825 (SeKA_C0096) | 60764..61378 | - | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| SEKA_RS29340 (SeKA_C0097) | 61378..64422 | - | 3045 | WP_001024751 | IncI1-type conjugal transfer protein TraU | traU |
| SEKA_RS29345 (SeKA_C0098) | 64512..65312 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| SEKA_RS29350 (SeKA_C0099) | 65296..65484 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| SEKA_RS29355 (SeKA_C0100) | 65548..65952 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| SEKA_RS29360 (SeKA_C0101) | 66003..66530 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| SEKA_RS29365 (SeKA_C0102) | 66530..67234 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| SEKA_RS29370 (SeKA_C0103) | 67234..68523 | - | 1290 | WP_001271997 | conjugal transfer protein TraO | traO |
| SEKA_RS29375 (SeKA_C0104) | 68526..69509 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| SEKA_RS29380 (SeKA_C0105) | 69520..70212 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| SEKA_RS29385 (SeKA_C0106) | 70209..70556 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| SEKA_RS29390 (SeKA_C0107) | 70574..74341 | - | 3768 | WP_001141535 | LPD7 domain-containing protein | - |
| SEKA_RS29395 (SeKA_C0108) | 74431..74982 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| SEKA_RS31830 (SeKA_C0109) | 74997..75287 | - | 291 | WP_001299214 | hypothetical protein | traK |
| SEKA_RS29400 (SeKA_C0110) | 75284..76432 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| SEKA_RS29405 (SeKA_C0111) | 76429..77247 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| SEKA_RS29410 (SeKA_C0112) | 77244..77702 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| SEKA_RS29415 (SeKA_C0114) | 78097..78681 | - | 585 | WP_000977517 | histidine phosphatase family protein | - |
| SEKA_RS29420 (SeKA_C0115) | 78741..79943 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| SEKA_RS29425 (SeKA_C0116) | 80029..80853 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| SEKA_RS29430 (SeKA_C0117) | 81004..82158 | - | 1155 | WP_001139958 | site-specific integrase | - |
| SEKA_RS34070 | 82744..82965 | + | 222 | Protein_93 | prepilin | - |
| SEKA_RS29435 (SeKA_C0118) | 82962..84386 | - | 1425 | WP_023278060 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| SEKA_RS31840 (SeKA_C0119) | 84386..85042 | - | 657 | WP_001193553 | prepilin peptidase | - |
| SEKA_RS29440 (SeKA_C0120) | 85027..85587 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| SEKA_RS29445 (SeKA_C0121) | 85597..86211 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| SEKA_RS29450 (SeKA_C0122) | 86229..87326 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| SEKA_RS29455 (SeKA_C0123) | 87339..88892 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| SEKA_RS29460 (SeKA_C0124) | 88903..89355 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| SEKA_RS29465 (SeKA_C0125) | 89342..90637 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| SEKA_RS29470 (SeKA_C0126) | 90630..92312 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| SEKA_RS29475 (SeKA_C0127) | 92326..92763 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| SEKA_RS31845 (SeKA_C0128) | 92763..92963 | - | 201 | Protein_104 | TcpQ domain-containing protein | - |
Host bacterium
| ID | 762 | GenBank | NC_011077 |
| Plasmid name | pCVM29188_101 | Incompatibility group | IncI1 |
| Plasmid size | 101461 bp | Coordinate of oriT [Strand] | 43719..43828 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188 |
Cargo genes
| Drug resistance gene | blaCMY-2 |
| Virulence gene | pathogenic E. coli (APEC) virulence factors |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |