Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113250 |
| Name | oriT_pRM101_2  |
| Organism | Salmonella enterica subsp. enterica serovar Heidelberg strain RM101 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP117350 (32292..32380 [-], 89 nt) |
| oriT length | 89 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 89 nt
>oriT_pRM101_2
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8500 | GenBank | WP_010891268 |
| Name | nikB_PQQ11_RS24425_pRM101_2 |
UniProt ID | A0A632VGA6 |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 103977.42 Da Isoelectric Point: 7.2753
>WP_010891268.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYIAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYIAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFLQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A632VGA6 |
Auxiliary protein
| ID | 4900 | GenBank | WP_001283947 |
| Name | WP_001283947_pRM101_2 |
UniProt ID | A0A142CMC2 |
| Length | 110 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12613.57 Da Isoelectric Point: 10.7463
>WP_001283947.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A142CMC2 |
T4CP
| ID | 9808 | GenBank | WP_001289276 |
| Name | trbC_PQQ11_RS24430_pRM101_2 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86941.11 Da Isoelectric Point: 6.7713
>WP_001289276.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 37758..75708
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PQQ11_RS24430 (PQQ11_24430) | 35474..37765 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| PQQ11_RS24435 (PQQ11_24435) | 37758..38828 | - | 1071 | WP_274898323 | IncI1-type conjugal transfer protein TrbB | trbB |
| PQQ11_RS24440 (PQQ11_24440) | 38847..40055 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| PQQ11_RS24445 (PQQ11_24445) | 40347..40499 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| PQQ11_RS24450 (PQQ11_24450) | 40571..40822 | - | 252 | WP_001291964 | hypothetical protein | - |
| PQQ11_RS24455 (PQQ11_24455) | 41321..41416 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| PQQ11_RS24460 (PQQ11_24460) | 41481..41657 | - | 177 | WP_001054904 | hypothetical protein | - |
| PQQ11_RS24465 (PQQ11_24465) | 42049..42258 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| PQQ11_RS24470 (PQQ11_24470) | 42330..42980 | - | 651 | WP_001178506 | plasmid IncI1-type surface exclusion protein ExcA | - |
| PQQ11_RS24475 (PQQ11_24475) | 43054..45222 | - | 2169 | WP_000698357 | DotA/TraY family protein | traY |
| PQQ11_RS24480 (PQQ11_24480) | 45319..45903 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| PQQ11_RS24485 (PQQ11_24485) | 45932..47134 | - | 1203 | WP_001189160 | IncI1-type conjugal transfer protein TraW | traW |
| PQQ11_RS24490 (PQQ11_24490) | 47101..47715 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| PQQ11_RS24495 (PQQ11_24495) | 47715..50759 | - | 3045 | WP_274898310 | IncI1-type conjugal transfer protein TraU | traU |
| PQQ11_RS24500 (PQQ11_24500) | 50849..51649 | - | 801 | WP_274898311 | IncI1-type conjugal transfer protein TraT | traT |
| PQQ11_RS24505 (PQQ11_24505) | 51633..51821 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| PQQ11_RS24510 (PQQ11_24510) | 51885..52289 | - | 405 | WP_000086959 | IncI1-type conjugal transfer protein TraR | traR |
| PQQ11_RS24515 (PQQ11_24515) | 52340..52867 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| PQQ11_RS24520 (PQQ11_24520) | 52867..53571 | - | 705 | WP_274898312 | IncI1-type conjugal transfer protein TraP | traP |
| PQQ11_RS24525 (PQQ11_24525) | 53571..54860 | - | 1290 | WP_001272000 | conjugal transfer protein TraO | traO |
| PQQ11_RS24530 (PQQ11_24530) | 54863..55846 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| PQQ11_RS24535 (PQQ11_24535) | 55857..56549 | - | 693 | WP_000138551 | DotI/IcmL family type IV secretion protein | traM |
| PQQ11_RS24540 (PQQ11_24540) | 56546..56893 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| PQQ11_RS24545 (PQQ11_24545) | 56911..60678 | - | 3768 | WP_001141541 | LPD7 domain-containing protein | - |
| PQQ11_RS24550 (PQQ11_24550) | 60768..61319 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| PQQ11_RS24555 (PQQ11_24555) | 61334..61624 | - | 291 | WP_001372180 | hypothetical protein | traK |
| PQQ11_RS24560 (PQQ11_24560) | 61621..62769 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| PQQ11_RS24565 (PQQ11_24565) | 62766..63584 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| PQQ11_RS24570 (PQQ11_24570) | 63581..64039 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| PQQ11_RS24575 (PQQ11_24575) | 64434..65018 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| PQQ11_RS24580 (PQQ11_24580) | 65078..66280 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| PQQ11_RS24585 (PQQ11_24585) | 66366..67190 | - | 825 | WP_001238929 | conjugal transfer protein TraE | traE |
| PQQ11_RS24590 (PQQ11_24590) | 67341..68493 | - | 1153 | Protein_76 | site-specific integrase | - |
| PQQ11_RS24595 (PQQ11_24595) | 68492..68791 | + | 300 | WP_274898313 | hypothetical protein | - |
| PQQ11_RS24600 (PQQ11_24600) | 69972..71204 | - | 1233 | WP_274898314 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| PQQ11_RS24605 (PQQ11_24605) | 71204..71860 | - | 657 | WP_001193553 | prepilin peptidase | - |
| PQQ11_RS24610 (PQQ11_24610) | 71845..72363 | - | 519 | WP_236920224 | lytic transglycosylase domain-containing protein | virB1 |
| PQQ11_RS24615 (PQQ11_24615) | 72414..73028 | - | 615 | WP_000959786 | type 4 pilus major pilin | - |
| PQQ11_RS24620 (PQQ11_24620) | 73046..74142 | - | 1097 | Protein_82 | type II secretion system F family protein | - |
| PQQ11_RS24625 (PQQ11_24625) | 74155..75708 | - | 1554 | WP_000362202 | GspE/PulE family protein | virB11 |
| PQQ11_RS24630 (PQQ11_24630) | 75719..76171 | - | 453 | WP_001247334 | type IV pilus biogenesis protein PilP | - |
| PQQ11_RS24635 (PQQ11_24635) | 76158..77453 | - | 1296 | WP_000752772 | type 4b pilus protein PilO2 | - |
| PQQ11_RS24640 (PQQ11_24640) | 77446..79128 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| PQQ11_RS24645 (PQQ11_24645) | 79142..79579 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| PQQ11_RS24650 (PQQ11_24650) | 79579..80646 | - | 1068 | WP_001302629 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 13685 | GenBank | NZ_CP117350 |
| Plasmid name | pRM101_2 | Incompatibility group | IncI1 |
| Plasmid size | 86233 bp | Coordinate of oriT [Strand] | 32292..32380 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Heidelberg strain RM101 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |