Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113232 |
| Name | oriT_pRM002_1  |
| Organism | Salmonella enterica subsp. enterica serovar Derby strain RM002 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP117318 (33521..33609 [-], 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_pRM002_1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8491 | GenBank | WP_274881822 |
| Name | nikB_PQQ14_RS23700_pRM002_1 |
UniProt ID | _ |
| Length | 898 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 898 a.a. Molecular weight: 103840.27 Da Isoelectric Point: 7.6059
>WP_274881822.1 IncI1-type relaxase NikB [Salmonella enterica]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSQAEQPHRSRFSRLVDYATRLRNESFVALVDV
MKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVRH
TLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCWV
HAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQKDGKF
LVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETES
LQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLTL
DNVNQLDGGWQPVPTDIFRQVTPTERFRGRRRESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGYS
ISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEPQ
AGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRKP
DLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPP
SYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSV
RFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAWH
NVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSQAEQPHRSRFSRLVDYATRLRNESFVALVDV
MKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVRH
TLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCWV
HAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQKDGKF
LVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETES
LQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLTL
DNVNQLDGGWQPVPTDIFRQVTPTERFRGRRRESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGYS
ISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEPQ
AGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRKP
DLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPP
SYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSV
RFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAWH
NVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 4891 | GenBank | WP_001283947 |
| Name | WP_001283947_pRM002_1 |
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 | 9797 | GenBank | WP_274881823 |
| Name | trbC_PQQ14_RS23705_pRM002_1 |
UniProt ID | _ |
| Length | 763 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 763 a.a. Molecular weight: 87003.18 Da Isoelectric Point: 6.7712
>WP_274881823.1 F-type conjugative transfer protein TrbC [Salmonella enterica]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKYNRPDWDGMY
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKYNRPDWDGMY
Protein domains
No domain identified.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 38984..77950
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PQQ14_RS23705 (PQQ14_23705) | 36700..38991 | - | 2292 | WP_274881823 | F-type conjugative transfer protein TrbC | - |
| PQQ14_RS23710 (PQQ14_23710) | 38984..40054 | - | 1071 | WP_000151583 | IncI1-type conjugal transfer protein TrbB | trbB |
| PQQ14_RS23715 (PQQ14_23715) | 40073..41281 | - | 1209 | WP_039005623 | IncI1-type conjugal transfer protein TrbA | trbA |
| PQQ14_RS23720 (PQQ14_23720) | 41573..41725 | + | 153 | WP_001331364 | Hok/Gef family protein | - |
| PQQ14_RS23725 (PQQ14_23725) | 41797..42048 | - | 252 | WP_001291964 | hypothetical protein | - |
| PQQ14_RS23730 (PQQ14_23730) | 42549..42644 | + | 96 | WP_000609148 | DinQ-like type I toxin DqlB | - |
| PQQ14_RS23735 (PQQ14_23735) | 42709..42885 | - | 177 | WP_001054904 | hypothetical protein | - |
| PQQ14_RS23740 (PQQ14_23740) | 43277..43486 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| PQQ14_RS23745 (PQQ14_23745) | 43558..44220 | - | 663 | WP_012783935 | plasmid IncI1-type surface exclusion protein ExcA | - |
| PQQ14_RS23750 (PQQ14_23750) | 44291..46459 | - | 2169 | WP_023518847 | DotA/TraY family protein | traY |
| PQQ14_RS23755 (PQQ14_23755) | 46556..47140 | - | 585 | WP_052896781 | IncI1-type conjugal transfer protein TraX | - |
| PQQ14_RS23760 (PQQ14_23760) | 47169..48371 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| PQQ14_RS23765 (PQQ14_23765) | 48338..48952 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| PQQ14_RS23770 (PQQ14_23770) | 48952..51996 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| PQQ14_RS23775 (PQQ14_23775) | 52086..52886 | - | 801 | WP_274881765 | IncI1-type conjugal transfer protein TraT | traT |
| PQQ14_RS23780 (PQQ14_23780) | 52870..53058 | - | 189 | WP_052896789 | putative conjugal transfer protein TraS | - |
| PQQ14_RS23785 (PQQ14_23785) | 53122..53526 | - | 405 | WP_000086960 | IncI1-type conjugal transfer protein TraR | traR |
| PQQ14_RS23790 (PQQ14_23790) | 53577..54104 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| PQQ14_RS23795 (PQQ14_23795) | 54104..54808 | - | 705 | WP_274881768 | IncI1-type conjugal transfer protein TraP | traP |
| PQQ14_RS23800 (PQQ14_23800) | 54808..56097 | - | 1290 | WP_001271994 | conjugal transfer protein TraO | traO |
| PQQ14_RS23805 (PQQ14_23805) | 56100..57083 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| PQQ14_RS23810 (PQQ14_23810) | 57094..57786 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| PQQ14_RS23815 (PQQ14_23815) | 57783..58130 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| PQQ14_RS23820 (PQQ14_23820) | 58148..61915 | - | 3768 | WP_052896792 | LPD7 domain-containing protein | - |
| PQQ14_RS23825 (PQQ14_23825) | 62005..62556 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| PQQ14_RS23830 (PQQ14_23830) | 62571..62861 | - | 291 | WP_072107178 | conjugal transfer protein | traK |
| PQQ14_RS23835 (PQQ14_23835) | 62858..64006 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| PQQ14_RS23840 (PQQ14_23840) | 64003..64821 | - | 819 | WP_000866663 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| PQQ14_RS23845 (PQQ14_23845) | 64818..65276 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| PQQ14_RS23850 (PQQ14_23850) | 65671..66255 | - | 585 | WP_016231299 | histidine phosphatase family protein | - |
| PQQ14_RS23855 (PQQ14_23855) | 66315..67517 | - | 1203 | WP_000976353 | conjugal transfer protein TraF | - |
| PQQ14_RS23860 (PQQ14_23860) | 67602..68426 | - | 825 | WP_001582597 | conjugal transfer protein TraE | traE |
| PQQ14_RS23865 (PQQ14_23865) | 68577..69731 | - | 1155 | WP_001139958 | tyrosine-type recombinase/integrase | - |
| PQQ14_RS24130 | 71808..72050 | + | 243 | Protein_82 | hypothetical protein | - |
| PQQ14_RS23870 (PQQ14_23870) | 72321..73469 | - | 1149 | WP_353739098 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| PQQ14_RS23875 (PQQ14_23875) | 73457..74113 | - | 657 | WP_001193549 | A24 family peptidase | - |
| PQQ14_RS23880 (PQQ14_23880) | 74098..74658 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| PQQ14_RS23885 (PQQ14_23885) | 74668..75282 | - | 615 | WP_000908226 | type 4 pilus major pilin | - |
| PQQ14_RS23890 (PQQ14_23890) | 75299..76384 | - | 1086 | WP_274881791 | type II secretion system F family protein | - |
| PQQ14_RS23895 (PQQ14_23895) | 76397..77950 | - | 1554 | WP_274881792 | GspE/PulE family protein | virB11 |
| PQQ14_RS23900 (PQQ14_23900) | 77961..78413 | - | 453 | WP_001247337 | type IV pilus biogenesis protein PilP | - |
| PQQ14_RS23905 (PQQ14_23905) | 78400..79695 | - | 1296 | WP_000752780 | type 4b pilus protein PilO2 | - |
| PQQ14_RS23910 (PQQ14_23910) | 79688..81370 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| PQQ14_RS23915 (PQQ14_23915) | 81384..81821 | - | 438 | WP_274881793 | type IV pilus biogenesis protein PilM | - |
| PQQ14_RS23920 (PQQ14_23920) | 81821..82888 | - | 1068 | WP_001360287 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 13667 | GenBank | NZ_CP117318 |
| Plasmid name | pRM002_1 | Incompatibility group | IncI1 |
| Plasmid size | 87713 bp | Coordinate of oriT [Strand] | 33521..33609 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Derby strain RM002 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |