Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 105277 |
| Name | oriT_pRHB10-C04_2  |
| Organism | Escherichia fergusonii strain RHB10-C04 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP057919 (63754..63842 [-], 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_pRHB10-C04_2
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3612 | GenBank | WP_181576135 |
| Name | nikB_HVW38_RS22410_pRHB10-C04_2 |
UniProt ID | _ |
| Length | 899 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104089.61 Da Isoelectric Point: 7.3473
>WP_181576135.1 IncI1-type relaxase NikB [Escherichia fergusonii]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNVLADKLDLIAPVLFWRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNVLADKLDLIAPVLFWRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 1618 | GenBank | WP_001283947 |
| Name | WP_001283947_pRHB10-C04_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 | 3575 | GenBank | WP_001289276 |
| Name | trbC_HVW38_RS22415_pRHB10-C04_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: 69220..105261
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HVW38_RS22415 (HVW38_22420) | 66936..69227 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HVW38_RS22420 (HVW38_22425) | 69220..70290 | - | 1071 | WP_001542508 | IncI1-type conjugal transfer protein TrbB | trbB |
| HVW38_RS22425 (HVW38_22430) | 70309..71517 | - | 1209 | WP_175237471 | IncI1-type conjugal transfer protein TrbA | trbA |
| HVW38_RS22430 (HVW38_22435) | 71809..71961 | + | 153 | WP_024179514 | Hok/Gef family protein | - |
| HVW38_RS22435 (HVW38_22440) | 72033..72284 | - | 252 | WP_001291965 | hypothetical protein | - |
| HVW38_RS22925 | 73409..73507 | + | 99 | WP_022630883 | DinQ-like type I toxin DqlB | - |
| HVW38_RS22440 (HVW38_22445) | 73954..74163 | - | 210 | WP_015059315 | hemolysin expression modulator Hha | - |
| HVW38_RS22445 (HVW38_22450) | 74261..74875 | - | 615 | WP_015059316 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HVW38_RS22450 (HVW38_22455) | 74951..77119 | - | 2169 | WP_181576136 | IncI1-type conjugal transfer membrane protein TraY | traY |
| HVW38_RS22455 (HVW38_22460) | 77216..77800 | - | 585 | WP_003566808 | IncI1-type conjugal transfer protein TraX | - |
| HVW38_RS22460 (HVW38_22465) | 77829..79031 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| HVW38_RS22465 (HVW38_22470) | 78998..79612 | - | 615 | WP_000337400 | IncI1-type conjugal transfer protein TraV | traV |
| HVW38_RS22470 (HVW38_22475) | 79612..82656 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| HVW38_RS22475 (HVW38_22480) | 82746..83546 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HVW38_RS22480 (HVW38_22485) | 83530..83718 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HVW38_RS22485 (HVW38_22490) | 83782..84186 | - | 405 | WP_000086957 | IncI1-type conjugal transfer protein TraR | traR |
| HVW38_RS22490 (HVW38_22495) | 84237..84764 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HVW38_RS22495 (HVW38_22500) | 84764..85468 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HVW38_RS22500 (HVW38_22505) | 85468..86757 | - | 1290 | WP_001271992 | conjugal transfer protein TraO | traO |
| HVW38_RS22505 (HVW38_22510) | 86760..87743 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| HVW38_RS22510 (HVW38_22515) | 87754..88446 | - | 693 | WP_181576137 | DotI/IcmL family type IV secretion protein | traM |
| HVW38_RS22515 (HVW38_22520) | 88443..88790 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HVW38_RS22520 (HVW38_22525) | 88808..92575 | - | 3768 | WP_181576138 | LPD7 domain-containing protein | - |
| HVW38_RS22525 (HVW38_22530) | 92665..93216 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| HVW38_RS22530 (HVW38_22535) | 93231..93521 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HVW38_RS22535 (HVW38_22540) | 93518..94666 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HVW38_RS22540 (HVW38_22545) | 94663..95481 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HVW38_RS22545 (HVW38_22550) | 95478..95936 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HVW38_RS22550 (HVW38_22555) | 96331..96915 | - | 585 | WP_181576139 | histidine phosphatase family protein | - |
| HVW38_RS22555 (HVW38_22560) | 96975..98177 | - | 1203 | WP_000976350 | conjugal transfer protein TraF | - |
| HVW38_RS22560 (HVW38_22565) | 98263..99086 | - | 824 | Protein_111 | conjugal transfer protein TraE | - |
| HVW38_RS22565 (HVW38_22570) | 99294..99419 | + | 126 | Protein_112 | transposase | - |
| HVW38_RS22570 (HVW38_22575) | 99476..100768 | - | 1293 | WP_181576140 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HVW38_RS22575 (HVW38_22580) | 100768..101424 | - | 657 | WP_001193549 | A24 family peptidase | - |
| HVW38_RS22580 (HVW38_22585) | 101409..101969 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| HVW38_RS22585 (HVW38_22590) | 101979..102593 | - | 615 | WP_062858101 | type 4 pilus major pilin | - |
| HVW38_RS22590 (HVW38_22595) | 102610..103695 | - | 1086 | WP_001208802 | type II secretion system F family protein | - |
| HVW38_RS22595 (HVW38_22600) | 103708..105261 | - | 1554 | WP_000362206 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HVW38_RS22600 (HVW38_22605) | 105272..105724 | - | 453 | WP_001247337 | type IV pilus biogenesis protein PilP | - |
| HVW38_RS22605 (HVW38_22610) | 105711..107006 | - | 1296 | WP_000752780 | type 4b pilus protein PilO2 | - |
| HVW38_RS22610 (HVW38_22615) | 106999..108681 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HVW38_RS22615 (HVW38_22620) | 108695..109132 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HVW38_RS22620 (HVW38_22625) | 109132..110199 | - | 1068 | WP_042012078 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 5715 | GenBank | NZ_CP057919 |
| Plasmid name | pRHB10-C04_2 | Incompatibility group | IncI1 |
| Plasmid size | 114980 bp | Coordinate of oriT [Strand] | 63754..63842 [-] |
| Host baterium | Escherichia fergusonii strain RHB10-C04 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |