Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100477 |
| Name | oriT_pSD107  |
| Organism | Salmonella enterica subsp. enterica serovar Derby |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_019137 (54168..54270 [-], 103 nt) |
| oriT length | 103 nt |
| IRs (inverted repeats) | IR1: 19..26, 30..37 (GTCGGGGC..GCCCTGAC) IR2: 44..58, 67..81 (GCAATTGTATAATCG..CGGTTATACAATTGC) |
| Location of nic site | 89..90 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 103 nt
>oriT_pSD107
TCAGCTCCTTACTGGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTCAGG
TCAGCTCCTTACTGGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 548 | GenBank | YP_006958004 |
| Name | NikB_pSD107 |
UniProt ID | K4K111 |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104018.47 Da Isoelectric Point: 7.3526
>YP_006958004.1 conjugal transfer relaxase protein NikB (plasmid) [Salmonella enterica subsp. enterica serovar Derby]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCLAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCLAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | K4K111 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 59636..97431
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTB39_RS00340 (pSD107_095) | 57352..59643 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HTB39_RS00345 (pSD107_096) | 59636..60706 | - | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| HTB39_RS00350 (pSD107_097) | 60725..61933 | - | 1209 | WP_000121274 | IncI1-type conjugal transfer protein TrbA | trbA |
| HTB39_RS00355 (pSD107_099) | 62225..62377 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| HTB39_RS00615 (pSD107_100) | 62449..62640 | - | 192 | WP_174715448 | hypothetical protein | - |
| HTB39_RS00610 | 63201..63296 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| HTB39_RS00365 (pSD107_102) | 63361..63642 | - | 282 | WP_015059947 | hypothetical protein | - |
| HTB39_RS00370 (pSD107_103) | 63927..64136 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HTB39_RS00375 (pSD107_104) | 64208..64870 | - | 663 | WP_000653334 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HTB39_RS00380 (pSD107_105) | 64935..67097 | - | 2163 | WP_000698351 | DotA/TraY family protein | traY |
| HTB39_RS00385 (pSD107_106) | 67194..67778 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| HTB39_RS00390 (pSD107_107) | 67807..69009 | - | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| HTB39_RS00395 (pSD107_108) | 68976..69590 | - | 615 | WP_000337398 | IncI1-type conjugal transfer protein TraV | traV |
| HTB39_RS00400 (pSD107_109) | 69590..72634 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| HTB39_RS00405 (pSD107_110) | 72724..73524 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HTB39_RS00410 (pSD107_111) | 73508..73696 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HTB39_RS00415 (pSD107_112) | 73760..74164 | - | 405 | WP_000086957 | IncI1-type conjugal transfer protein TraR | traR |
| HTB39_RS00420 (pSD107_113) | 74215..74742 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HTB39_RS00425 (pSD107_114) | 74742..75446 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HTB39_RS00430 (pSD107_115) | 75446..76735 | - | 1290 | WP_001272005 | conjugal transfer protein TraO | traO |
| HTB39_RS00435 (pSD107_116) | 76738..77721 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| HTB39_RS00440 (pSD107_117) | 77732..78424 | - | 693 | WP_000138548 | DotI/IcmL family type IV secretion protein | traM |
| HTB39_RS00445 (pSD107_118) | 78421..78768 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HTB39_RS00450 (pSD107_119) | 78786..82553 | - | 3768 | WP_001141529 | LPD7 domain-containing protein | - |
| HTB39_RS00455 (pSD107_120) | 82643..83194 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| HTB39_RS00460 (pSD107_121) | 83209..83499 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HTB39_RS00465 (pSD107_122) | 83496..84644 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HTB39_RS00470 (pSD107_123) | 84641..85459 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HTB39_RS00475 (pSD107_124) | 85456..85914 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HTB39_RS00480 (pSD107_125) | 86309..86893 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HTB39_RS00485 (pSD107_126) | 86953..88155 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| HTB39_RS00490 (pSD107_127) | 88240..89064 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| HTB39_RS00495 (pSD107_128) | 89215..90369 | - | 1155 | WP_001139957 | site-specific integrase | - |
| HTB39_RS00500 (pSD107_129) | 90368..90679 | + | 312 | WP_000958120 | hypothetical protein | - |
| HTB39_RS00605 | 91488..91637 | + | 150 | WP_001302708 | hypothetical protein | - |
| HTB39_RS00510 (pSD107_133) | 91634..92926 | - | 1293 | WP_001417545 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HTB39_RS00515 (pSD107_134) | 92926..93581 | - | 656 | Protein_104 | prepilin peptidase | - |
| HTB39_RS00520 (pSD107_135) | 93566..94126 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HTB39_RS00525 (pSD107_136) | 94136..94750 | - | 615 | WP_000959785 | type 4 pilus major pilin | - |
| HTB39_RS00530 (pSD107_137) | 94768..95865 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| HTB39_RS00535 (pSD107_138) | 95878..97431 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HTB39_RS00540 (pSD107_139) | 97442..97894 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| HTB39_RS00545 (pSD107_140) | 97881..99176 | - | 1296 | WP_000752774 | type 4b pilus protein PilO2 | - |
| HTB39_RS00550 (pSD107_141) | 99169..100852 | - | 1684 | Protein_111 | PilN family type IVB pilus formation outer membrane protein | - |
| HTB39_RS00555 (pSD107_142) | 100866..101303 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HTB39_RS00560 (pSD107_143) | 101303..102370 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 938 | GenBank | NC_019137 |
| Plasmid name | pSD107 | Incompatibility group | IncI1 |
| Plasmid size | 107637 bp | Coordinate of oriT [Strand] | 54168..54270 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Derby |
Cargo genes
| Drug resistance gene | sul1, qacE, ant(3'')-Ia, dfrA1, aph(6)-Id, aph(3'')-Ib, sul2, blaTEM-1B |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |