Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100731 |
| Name | oriT_pDM01  |
| Organism | Salmonella enterica subsp. enterica serovar Ouakam isolate GTN-01 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP012039 (70231..70340 [-], 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_pDM01
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 803 | GenBank | WP_069924919 |
| Name | NikB_pDM01 |
UniProt ID | _ |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103995.33 Da Isoelectric Point: 7.3426
>WP_069924919.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPVLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRASVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPVLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRASVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 75700..107840
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| AC247_RS24930 (AC247_25005) | 73416..75707 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| AC247_RS24935 (AC247_25010) | 75700..76770 | - | 1071 | WP_046340328 | IncI1-type conjugal transfer protein TrbB | trbB |
| AC247_RS24940 (AC247_25015) | 76789..77997 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| AC247_RS24945 (AC247_25020) | 78304..79389 | - | 1086 | WP_000080543 | protein finQ | - |
| AC247_RS24950 (AC247_25025) | 79710..79862 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| AC247_RS24955 (AC247_25030) | 79934..80185 | - | 252 | WP_001291965 | hypothetical protein | - |
| AC247_RS27945 | 81109..81285 | - | 177 | WP_001054900 | hypothetical protein | - |
| AC247_RS24960 (AC247_25035) | 81494..81703 | - | 210 | WP_001140545 | hemolysin expression modulator Hha | - |
| AC247_RS24965 (AC247_25040) | 81801..82415 | - | 615 | WP_000578649 | plasmid IncI1-type surface exclusion protein ExcA | - |
| AC247_RS24970 (AC247_25045) | 82491..84659 | - | 2169 | WP_000698360 | IncI1-type conjugal transfer membrane protein TraY | traY |
| AC247_RS24975 (AC247_25050) | 84756..85340 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| AC247_RS24980 (AC247_25055) | 85369..86571 | - | 1203 | WP_001189159 | IncI1-type conjugal transfer protein TraW | traW |
| AC247_RS26900 | 86538..87152 | - | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| AC247_RS24985 (AC247_25060) | 87152..90196 | - | 3045 | WP_001024752 | IncI1-type conjugal transfer protein TraU | traU |
| AC247_RS24990 (AC247_25065) | 90286..91086 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| AC247_RS24995 (AC247_25070) | 91070..91258 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| AC247_RS25000 (AC247_25075) | 91322..91726 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| AC247_RS25005 (AC247_25080) | 91777..92304 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| AC247_RS25010 (AC247_25085) | 92304..93008 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| AC247_RS25015 (AC247_25090) | 93008..94297 | - | 1290 | WP_001271997 | conjugal transfer protein TraO | traO |
| AC247_RS25020 (AC247_25095) | 94300..95283 | - | 984 | WP_001191878 | IncI1-type conjugal transfer protein TraN | traN |
| AC247_RS25025 (AC247_25100) | 95294..95986 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| AC247_RS25030 (AC247_25105) | 95983..96330 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| AC247_RS25035 (AC247_25110) | 96348..100115 | - | 3768 | WP_001141534 | LPD7 domain-containing protein | - |
| AC247_RS25040 (AC247_25115) | 100205..100756 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| AC247_RS26905 | 100771..101061 | - | 291 | WP_001299214 | hypothetical protein | traK |
| AC247_RS25045 (AC247_25120) | 101058..102206 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| AC247_RS25050 (AC247_25125) | 102203..103021 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| AC247_RS25055 (AC247_25130) | 103018..103476 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| AC247_RS25060 (AC247_25135) | 103871..104206 | - | 336 | Protein_111 | lipopolysaccharide core heptose(II)-phosphate phosphatase | - |
| AC247_RS25070 (AC247_25145) | 104298..105526 | + | 1229 | WP_089541817 | IS3 family transposase | - |
| AC247_RS28350 | 105537..105668 | - | 132 | Protein_113 | histidine phosphatase family protein | - |
| AC247_RS25075 (AC247_25150) | 105728..106930 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| AC247_RS25080 (AC247_25155) | 107016..107840 | - | 825 | WP_001238927 | conjugal transfer protein TraE | traE |
| AC247_RS25085 (AC247_25160) | 107991..109145 | - | 1155 | WP_001139957 | site-specific integrase | - |
Host bacterium
| ID | 1191 | GenBank | NZ_CP012039 |
| Plasmid name | pDM01 | Incompatibility group | IncI1 |
| Plasmid size | 109715 bp | Coordinate of oriT [Strand] | 70231..70340 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Ouakam isolate GTN-01 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |