Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100017 |
| Name | oriT_R64  |
| Organism | Salmonella enterica subsp. enterica serovar Typhimurium |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_005014 (_) |
| oriT length | 92 nt |
| IRs (inverted repeats) | 8..bp: 6..13, 17..24 (GTCGGGGC..GCCCTGAC) 17..bp: 31..47, 54..70 (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC) |
| Location of nic site | 78..79 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | minimal oriT sequence |
oriT sequence
Download Length: 92 nt
>oriT_R64
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCGGG
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCGGG
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Furuya N et al. (1991) Determination of the nick site at oriT of IncI1 plasmid R64: global similarity of oriT structures of IncI1 and IncP plasmids. J Bacteriol. 173(20):6612-7. [PMID:1917882]
[2] Komano T et al. (1990) Transfer region of IncI1 plasmid R64 and role of shufflon in R64 transfer. J Bacteriol. 172(5):2230-5. [PMID:1970558]
Relaxosome
This oriT is a component of a relaxosome.
| Relaxosome name | RelaxosomeR64  |
| oriT | oriT_R64 |
| Relaxase | NikB_R64 (MOBP) |
| Auxiliary protein | NikA_R64 |
Reference
[1] Furuya N et al. (1991) Determination of the nick site at oriT of IncI1 plasmid R64: global similarity of oriT structures of IncI1 and IncP plasmids. J Bacteriol. 173(20):6612-7. [PMID:1917882]
[2] Komano T et al. (1990) Transfer region of IncI1 plasmid R64 and role of shufflon in R64 transfer. J Bacteriol. 172(5):2230-5. [PMID:1970558]
Relaxase
| ID | 16 | GenBank | NP_863436 |
| Name | NikB_R64 |
UniProt ID | Q79VV7 |
| Length | 899 a.a. | PDB ID | |
| Note | to recognize the conserved nick region sequence | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104010.41 Da Isoelectric Point: 7.4265
>NP_863436.1 hypothetical protein R64_p081 (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q79VV7 |
Reference
[1] Furuya N et al. (1991) Determination of the nick site at oriT of IncI1 plasmid R64: global similarity of oriT structures of IncI1 and IncP plasmids. J Bacteriol. 173(20):6612-7. [PMID:1917882]
Auxiliary protein
| ID | 26 | GenBank | NP_863435 |
| Name | NikA_R64 |
UniProt ID | Q79VV8 |
| Length | 110 a.a. | PDB ID | _ |
| Note | an oriT-binding protein (to recognize the 17-bp repeat A sequence) | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12613.57 Da Isoelectric Point: 10.7463
>NP_863435.1 hypothetical protein R64_p080 (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q79VV8 |
Reference
[1] Furuya N et al. (1991) Determination of the nick site at oriT of IncI1 plasmid R64: global similarity of oriT structures of IncI1 and IncP plasmids. J Bacteriol. 173(20):6612-7. [PMID:1917882]
T4CP
| ID | 16 | GenBank | NP_863437 |
| Name | TrbC_R64 |
UniProt ID | Q79VV6 |
| Length | 763 a.a. | PDB ID | _ |
| Note | NP_863437 hypothetical protein R64_p082 (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium] | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 86941.11 Da Isoelectric Point: 6.7713
>NP_863437.1 hypothetical protein R64_p082 (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
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
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q79VV6 |
Reference
[1] Ding Z et al. (2003) The outs and ins of bacterial type IV secretion substrates. Trends Microbiol. 11(11):527-35. [PMID:14607070]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 72411..110720
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| QBL16_RS00405 (R64_p082) | 70127..72418 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| QBL16_RS00410 (R64_p083) | 72411..73481 | - | 1071 | WP_000151582 | IncI1-type conjugal transfer protein TrbB | trbB |
| QBL16_RS00415 (R64_p084) | 73500..74708 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| QBL16_RS00420 (R64_p086) | 75000..75152 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| QBL16_RS00425 (R64_RS00430) | 75224..75475 | - | 252 | WP_001291964 | hypothetical protein | - |
| QBL16_RS00430 | 75974..76069 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| QBL16_RS00435 (R64_RS00435) | 76134..76310 | - | 177 | WP_001054897 | hypothetical protein | - |
| QBL16_RS00440 (R64_RS00440) | 76702..76911 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| QBL16_RS00445 (R64_p087) | 76983..77645 | - | 663 | WP_000644796 | plasmid IncI1-type surface exclusion protein ExcA | - |
| QBL16_RS00450 (R64_p089) | 77716..79884 | - | 2169 | WP_000698354 | DotA/TraY family protein | traY |
| QBL16_RS00455 (R64_p090) | 79981..80565 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| QBL16_RS00460 (R64_p091) | 80594..81796 | - | 1203 | WP_001385654 | IncI1-type conjugal transfer protein TraW | traW |
| QBL16_RS00465 (R64_p092) | 81763..82377 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| QBL16_RS00470 (R64_p093) | 82377..85421 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| QBL16_RS00475 (R64_p094) | 85511..86311 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| QBL16_RS00480 (R64_p095) | 86295..86483 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| QBL16_RS00485 (R64_p096) | 86547..86951 | - | 405 | WP_000086958 | IncI1-type conjugal transfer protein TraR | traR |
| QBL16_RS00490 (R64_p097) | 87002..87529 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| QBL16_RS00495 (R64_p098) | 87529..88233 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| QBL16_RS00500 (R64_p099) | 88233..89522 | - | 1290 | WP_001272003 | conjugal transfer protein TraO | traO |
| QBL16_RS00505 (R64_p100) | 89525..90508 | - | 984 | WP_001191877 | IncI1-type conjugal transfer protein TraN | traN |
| QBL16_RS00510 (R64_p101) | 90519..91211 | - | 693 | WP_000138550 | DotI/IcmL family type IV secretion protein | traM |
| QBL16_RS00515 (R64_p102) | 91208..91555 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| QBL16_RS00520 (R64_p103) | 91573..95340 | - | 3768 | WP_011117609 | LPD7 domain-containing protein | - |
| QBL16_RS00525 (R64_p105) | 95430..95981 | - | 552 | WP_000014583 | phospholipase D family protein | - |
| QBL16_RS00530 (R64_p106) | 95996..96286 | - | 291 | WP_011117611 | hypothetical protein | traK |
| QBL16_RS00535 (R64_p107) | 96283..97431 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| QBL16_RS00540 (R64_p108) | 97428..98246 | - | 819 | WP_000646098 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| QBL16_RS00545 (R64_p109) | 98243..98701 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| QBL16_RS00550 (R64_p110) | 99096..99680 | - | 585 | WP_000977522 | histidine phosphatase family protein | - |
| QBL16_RS00555 (R64_p111) | 99740..100942 | - | 1203 | WP_000976351 | conjugal transfer protein TraF | - |
| QBL16_RS00560 (R64_p112) | 101027..101851 | - | 825 | WP_001238939 | conjugal transfer protein TraE | traE |
| QBL16_RS00565 (R64_p113) | 102002..103156 | - | 1155 | WP_001139957 | site-specific integrase | - |
| QBL16_RS00570 (R64_p114) | 103140..103466 | + | 327 | WP_001213803 | hypothetical protein | - |
| QBL16_RS00665 (R64_p119) | 104572..104793 | + | 222 | Protein_114 | prepilin | - |
| QBL16_RS00575 (R64_p120) | 104790..106214 | - | 1425 | WP_001389385 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| QBL16_RS00580 (R64_p121) | 106214..106870 | - | 657 | WP_001193553 | prepilin peptidase | - |
| QBL16_RS00585 (R64_p122) | 106855..107415 | - | 561 | WP_000014116 | lytic transglycosylase domain-containing protein | virB1 |
| QBL16_RS00590 (R64_p123) | 107425..108039 | - | 615 | WP_001696543 | type 4 pilus major pilin | - |
| QBL16_RS00595 (R64_p124) | 108057..109154 | - | 1098 | WP_001208805 | type II secretion system F family protein | - |
| QBL16_RS00600 (R64_p125) | 109167..110720 | - | 1554 | WP_000362202 | ATPase, T2SS/T4P/T4SS family | virB11 |
| QBL16_RS00605 (R64_p126) | 110731..111183 | - | 453 | WP_001247336 | type IV pilus biogenesis protein PilP | - |
| QBL16_RS00610 (R64_p127) | 111170..112465 | - | 1296 | WP_001696544 | type 4b pilus protein PilO2 | - |
| QBL16_RS00615 (R64_p128) | 112458..114140 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| QBL16_RS00620 (R64_p129) | 114154..114591 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| QBL16_RS00625 (R64_p130) | 114591..115658 | - | 1068 | WP_000742600 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 16 | GenBank | NC_005014 |
| Plasmid name | R64 | Incompatibility group | IncI1 |
| Plasmid size | 120826 bp | Coordinate of oriT [Strand] | 66951..67033 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Typhimurium |
Cargo genes
| Drug resistance gene | tet(B), aph(3'')-Ib, aph(6)-Id |
| Virulence gene | - |
| Metal resistance gene | arsR, arsD, arsA, arsB, arsC, arsH |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |