Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100790 |
| Name | oriT_pSTY1-1898  |
| Organism | Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP014972 (37338..37447 [-], 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_pSTY1-1898
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 862 | GenBank | WP_071921283 |
| Name | NikB_pSTY1-1898 |
UniProt ID | _ |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103977.49 Da Isoelectric Point: 7.1635
>WP_071921283.1 IncI1-type relaxase NikB [Salmonella enterica]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGLLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGELVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFERDPRMGFEPEGNDGQFNQVFAEMVAW
YNVTGFSEHGNYVITRPDVDQHREVSERGYRNYMDSNTYRDGTQPVQDSENRWEPPTPV
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGLLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGELVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFERDPRMGFEPEGNDGQFNQVFAEMVAW
YNVTGFSEHGNYVITRPDVDQHREVSERGYRNYMDSNTYRDGTQPVQDSENRWEPPTPV
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 48383..86425
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| AX01_RS26365 (AX01_23835) | 44679..45314 | - | 636 | WP_063320176 | CPBP family intramembrane glutamic endopeptidase | - |
| AX01_RS24520 (AX01_23845) | 46099..48390 | - | 2292 | WP_072279317 | F-type conjugative transfer protein TrbC | - |
| AX01_RS24525 (AX01_23850) | 48383..49453 | - | 1071 | WP_023225282 | IncI1-type conjugal transfer protein TrbB | trbB |
| AX01_RS24530 (AX01_23855) | 49472..50680 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| AX01_RS24535 (AX01_23860) | 50972..51124 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| AX01_RS24540 (AX01_23865) | 51196..51447 | - | 252 | WP_001291965 | hypothetical protein | - |
| AX01_RS25925 | 52371..52547 | - | 177 | WP_001054900 | hypothetical protein | - |
| AX01_RS24550 (AX01_23870) | 52939..53148 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| AX01_RS24555 (AX01_23875) | 53220..53882 | - | 663 | WP_000644794 | plasmid IncI1-type surface exclusion protein ExcA | - |
| AX01_RS24560 (AX01_23880) | 53953..56121 | - | 2169 | WP_000698368 | DotA/TraY family protein | traY |
| AX01_RS24565 (AX01_23885) | 56218..56802 | - | 585 | WP_001037985 | IncI1-type conjugal transfer protein TraX | - |
| AX01_RS24570 (AX01_23890) | 56831..58033 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| AX01_RS24575 (AX01_25775) | 58000..58614 | - | 615 | WP_000337400 | IncI1-type conjugal transfer protein TraV | traV |
| AX01_RS24580 (AX01_23895) | 58614..61658 | - | 3045 | WP_063320177 | IncI1-type conjugal transfer protein TraU | traU |
| AX01_RS24585 (AX01_23900) | 61748..62548 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| AX01_RS24590 (AX01_23905) | 62532..62720 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| AX01_RS24595 (AX01_23910) | 62784..63188 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| AX01_RS24600 (AX01_23915) | 63239..63766 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| AX01_RS24605 (AX01_23920) | 63766..64470 | - | 705 | WP_042012199 | IncI1-type conjugal transfer protein TraP | traP |
| AX01_RS24610 (AX01_23925) | 64470..65759 | - | 1290 | WP_001271991 | conjugal transfer protein TraO | traO |
| AX01_RS24615 (AX01_23930) | 65762..66745 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| AX01_RS24620 (AX01_23935) | 66756..67448 | - | 693 | WP_001685183 | DotI/IcmL family type IV secretion protein | traM |
| AX01_RS24625 (AX01_23940) | 67445..67792 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| AX01_RS24630 (AX01_23945) | 67810..71577 | - | 3768 | WP_063320178 | LPD7 domain-containing protein | - |
| AX01_RS24635 (AX01_23950) | 71667..72218 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| AX01_RS24640 (AX01_25780) | 72233..72523 | - | 291 | WP_001314267 | hypothetical protein | traK |
| AX01_RS24645 (AX01_23955) | 72520..73668 | - | 1149 | WP_063320179 | plasmid transfer ATPase TraJ | virB11 |
| AX01_RS24650 (AX01_23960) | 73665..74483 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| AX01_RS24655 (AX01_23965) | 74480..74938 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| AX01_RS24660 (AX01_23970) | 75333..75917 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| AX01_RS24665 (AX01_23975) | 75977..77179 | - | 1203 | WP_063320180 | conjugal transfer protein TraF | - |
| AX01_RS24670 (AX01_23980) | 77265..78089 | - | 825 | WP_022630873 | conjugal transfer protein TraE | traE |
| AX01_RS24675 (AX01_23985) | 78240..79394 | - | 1155 | WP_001139955 | site-specific integrase | - |
| AX01_RS26225 (AX01_25785) | 79393..79746 | + | 354 | WP_001393368 | hypothetical protein | - |
| AX01_RS25855 | 80382..80630 | + | 249 | WP_001349157 | hypothetical protein | - |
| AX01_RS24700 (AX01_23990) | 80627..81919 | - | 1293 | WP_001417545 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| AX01_RS24705 (AX01_25805) | 81919..82575 | - | 657 | WP_069200671 | prepilin peptidase | - |
| AX01_RS24710 (AX01_23995) | 82560..83120 | - | 561 | WP_063320181 | lytic transglycosylase domain-containing protein | virB1 |
| AX01_RS24715 (AX01_24000) | 83130..83744 | - | 615 | WP_063320182 | type 4 pilus major pilin | - |
| AX01_RS24720 (AX01_24005) | 83762..84859 | - | 1098 | WP_063320183 | type II secretion system F family protein | - |
| AX01_RS24725 (AX01_24010) | 84872..86425 | - | 1554 | WP_023166903 | ATPase, T2SS/T4P/T4SS family | virB11 |
| AX01_RS24730 (AX01_24015) | 86436..86888 | - | 453 | WP_001247870 | type IV pilus biogenesis protein PilP | - |
| AX01_RS24735 (AX01_24020) | 86875..88170 | - | 1296 | WP_063320184 | type 4b pilus protein PilO2 | - |
| AX01_RS24740 (AX01_24025) | 88163..89845 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| AX01_RS24745 (AX01_24030) | 89859..90296 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| AX01_RS24750 (AX01_24035) | 90296..91363 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 1250 | GenBank | NZ_CP014972 |
| Plasmid name | pSTY1-1898 | Incompatibility group | IncI1 |
| Plasmid size | 95780 bp | Coordinate of oriT [Strand] | 37338..37447 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |