Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100521 |
| Name | oriT_pKHSB1  |
| Organism | Shigella sonnei |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_020991 (92348..92457 [+], 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_pKHSB1
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 592 | GenBank | YP_007749339 |
| Name | Relaxase_pKHSB1 |
UniProt ID | N0GUP8 |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104070.55 Da Isoelectric Point: 7.3623
>YP_007749339.1 relaxase (plasmid) [Shigella sonnei]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | N0GUP8 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 47774..86988
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HXG86_RS00280 (ST624_p3085) | 42836..43903 | + | 1068 | WP_012783947 | type IV pilus biogenesis lipoprotein PilL | - |
| HXG86_RS00285 (ST624_p3071) | 43903..44340 | + | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HXG86_RS00290 (ST624_p3070) | 44354..46036 | + | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HXG86_RS00295 (ST624_p3069) | 46029..47324 | + | 1296 | WP_012783946 | type 4b pilus protein PilO2 | - |
| HXG86_RS00300 (ST624_p3068) | 47311..47763 | + | 453 | WP_012783945 | type IV pilus biogenesis protein PilP | - |
| HXG86_RS00305 (ST624_p3067) | 47774..49327 | + | 1554 | WP_001492932 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HXG86_RS00310 (ST624_p3066) | 49340..50437 | + | 1098 | WP_001492931 | type II secretion system F family protein | - |
| HXG86_RS00315 (ST624_p3065) | 50455..51069 | + | 615 | WP_001542527 | type 4 pilus major pilin | - |
| HXG86_RS00320 (ST624_p3064) | 51079..51639 | + | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| HXG86_RS00325 (ST624_p3063) | 51624..52280 | + | 657 | WP_001193553 | prepilin peptidase | - |
| HXG86_RS00330 (ST624_p3062) | 52280..53704 | + | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HXG86_RS00575 | 53701..53925 | - | 225 | Protein_67 | hypothetical protein | - |
| HXG86_RS00555 | 53971..54173 | + | 203 | Protein_68 | hypothetical protein | - |
| HXG86_RS00560 | 54468..54836 | - | 369 | WP_015059923 | hypothetical protein | - |
| HXG86_RS00350 (ST624_p3060) | 54820..55974 | + | 1155 | WP_001139955 | site-specific integrase | - |
| HXG86_RS00355 (ST624_p3031) | 56125..56949 | + | 825 | WP_001238932 | conjugal transfer protein TraE | traE |
| HXG86_RS00360 (ST624_p3089) | 57035..58237 | + | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| HXG86_RS00365 (ST624_p3053) | 58297..58881 | + | 585 | WP_000977522 | histidine phosphatase family protein | - |
| HXG86_RS00370 (ST624_p3032) | 59275..59733 | + | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HXG86_RS00375 (ST624_p3090) | 59730..60548 | + | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HXG86_RS00380 (ST624_p3052) | 60545..61693 | + | 1149 | WP_001024971 | plasmid transfer ATPase TraJ | virB11 |
| HXG86_RS00385 (ST624_p3051) | 61690..61980 | + | 291 | WP_001314267 | hypothetical protein | traK |
| HXG86_RS00390 (ST624_p3084) | 61995..62546 | + | 552 | WP_012783942 | phospholipase D family protein | - |
| HXG86_RS00395 (ST624_p3061) | 62636..66403 | + | 3768 | WP_012783940 | LPD7 domain-containing protein | - |
| HXG86_RS00400 (ST624_p3050) | 66421..66768 | + | 348 | WP_001055900 | conjugal transfer protein | traL |
| HXG86_RS00405 (ST624_p3049) | 66765..67457 | + | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| HXG86_RS00410 (ST624_p3048) | 67468..68451 | + | 984 | WP_001191880 | IncI1-type conjugal transfer protein TraN | traN |
| HXG86_RS00415 (ST624_p3044) | 68454..69743 | + | 1290 | WP_011264042 | conjugal transfer protein TraO | traO |
| HXG86_RS00420 (ST624_p3043) | 69743..70447 | + | 705 | WP_001493811 | IncI1-type conjugal transfer protein TraP | traP |
| HXG86_RS00425 (ST624_p3042) | 70447..70974 | + | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HXG86_RS00430 (ST624_p3041) | 71025..71429 | + | 405 | WP_000086965 | IncI1-type conjugal transfer protein TraR | traR |
| HXG86_RS00435 (ST624_p3040) | 71493..71681 | + | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HXG86_RS00440 (ST624_p3039) | 71665..72465 | + | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HXG86_RS00445 (ST624_p3038) | 72555..75599 | + | 3045 | WP_012783939 | IncI1-type conjugal transfer protein TraU | traU |
| HXG86_RS00450 (ST624_p3037) | 75599..76213 | + | 615 | WP_000337394 | IncI1-type conjugal transfer protein TraV | traV |
| HXG86_RS00455 (ST624_p3036) | 76180..77382 | + | 1203 | WP_012783938 | IncI1-type conjugal transfer protein TraW | traW |
| HXG86_RS00460 (ST624_p3034) | 77411..77995 | + | 585 | WP_012783937 | conjugal transfer protein TraX | - |
| HXG86_RS00465 (ST624_p3033) | 78092..80260 | + | 2169 | WP_015508354 | DotA/TraY family protein | traY |
| HXG86_RS00470 (ST624_p3087) | 80331..80993 | + | 663 | WP_012783935 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HXG86_RS00475 (ST624_p3091) | 81065..81274 | - | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HXG86_RS00480 | 81558..81842 | + | 285 | WP_014640317 | hypothetical protein | - |
| HXG86_RS00565 | 81907..82002 | - | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| HXG86_RS00490 (ST624_p3094) | 82503..82754 | + | 252 | WP_001291964 | hypothetical protein | - |
| HXG86_RS00495 (ST624_p3074) | 82826..82978 | - | 153 | WP_001387489 | Hok/Gef family protein | - |
| HXG86_RS00500 (ST624_p3095) | 83605..84384 | + | 780 | WP_275450201 | protein FinQ | - |
| HXG86_RS00505 (ST624_p3047) | 84691..85899 | + | 1209 | WP_001703845 | IncI1-type conjugal transfer protein TrbA | trbA |
| HXG86_RS00510 (ST624_p3046) | 85918..86988 | + | 1071 | WP_012783932 | IncI1-type conjugal transfer protein TrbB | trbB |
| HXG86_RS00515 (ST624_p3045) | 86981..89272 | + | 2292 | WP_012783931 | F-type conjugative transfer protein TrbC | - |
Host bacterium
| ID | 982 | GenBank | NC_020991 |
| Plasmid name | pKHSB1 | Incompatibility group | IncI1 |
| Plasmid size | 94089 bp | Coordinate of oriT [Strand] | 92348..92457 [+] |
| Host baterium | Shigella sonnei |
Cargo genes
| Drug resistance gene | blaTEM-1B, blaCTX-M-15 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrVA2 |