Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 105302 |
| Name | oriT_pRHB33-C07_3  |
| Organism | Escherichia fergusonii strain RHB33-C07 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP057212 (54368..54456 [-], 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_pRHB33-C07_3
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3624 | GenBank | WP_181576135 |
| Name | nikB_HVZ09_RS24140_pRHB33-C07_3 |
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 | 1628 | GenBank | WP_001283947 |
| Name | WP_001283947_pRHB33-C07_3 |
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 | 3591 | GenBank | WP_001289276 |
| Name | trbC_HVZ09_RS24145_pRHB33-C07_3 |
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: 59834..95248
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HVZ09_RS24145 (HVZ09_24100) | 57550..59841 | - | 2292 | WP_001289276 | F-type conjugative transfer protein TrbC | - |
| HVZ09_RS24150 (HVZ09_24105) | 59834..60904 | - | 1071 | WP_001542508 | IncI1-type conjugal transfer protein TrbB | trbB |
| HVZ09_RS24155 (HVZ09_24110) | 60923..62131 | - | 1209 | WP_175237471 | IncI1-type conjugal transfer protein TrbA | trbA |
| HVZ09_RS24160 (HVZ09_24115) | 62423..62575 | + | 153 | WP_024179514 | Hok/Gef family protein | - |
| HVZ09_RS24165 (HVZ09_24120) | 62647..62898 | - | 252 | WP_001291965 | hypothetical protein | - |
| HVZ09_RS24805 | 63396..63494 | + | 99 | WP_022630883 | DinQ-like type I toxin DqlB | - |
| HVZ09_RS24170 (HVZ09_24125) | 63941..64150 | - | 210 | WP_015059315 | hemolysin expression modulator Hha | - |
| HVZ09_RS24175 (HVZ09_24130) | 64248..64862 | - | 615 | WP_181667535 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HVZ09_RS24180 (HVZ09_24135) | 64938..67106 | - | 2169 | WP_181667536 | IncI1-type conjugal transfer membrane protein TraY | traY |
| HVZ09_RS24185 (HVZ09_24140) | 67203..67787 | - | 585 | WP_003566808 | IncI1-type conjugal transfer protein TraX | - |
| HVZ09_RS24190 (HVZ09_24145) | 67816..69018 | - | 1203 | WP_001189156 | IncI1-type conjugal transfer protein TraW | traW |
| HVZ09_RS24195 (HVZ09_24150) | 68985..69599 | - | 615 | WP_000337400 | IncI1-type conjugal transfer protein TraV | traV |
| HVZ09_RS24200 (HVZ09_24155) | 69599..72643 | - | 3045 | WP_001024780 | IncI1-type conjugal transfer protein TraU | traU |
| HVZ09_RS24205 (HVZ09_24160) | 72733..73533 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HVZ09_RS24210 (HVZ09_24165) | 73517..73705 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HVZ09_RS24215 (HVZ09_24170) | 73769..74173 | - | 405 | WP_000086957 | IncI1-type conjugal transfer protein TraR | traR |
| HVZ09_RS24220 (HVZ09_24175) | 74224..74751 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HVZ09_RS24225 (HVZ09_24180) | 74751..75455 | - | 705 | WP_000801920 | IncI1-type conjugal transfer protein TraP | traP |
| HVZ09_RS24230 (HVZ09_24185) | 75455..76744 | - | 1290 | WP_001271992 | conjugal transfer protein TraO | traO |
| HVZ09_RS24235 (HVZ09_24190) | 76747..77730 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| HVZ09_RS24240 (HVZ09_24195) | 77741..78433 | - | 693 | WP_181576137 | DotI/IcmL family type IV secretion protein | traM |
| HVZ09_RS24245 (HVZ09_24200) | 78430..78777 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HVZ09_RS24250 (HVZ09_24205) | 78795..82562 | - | 3768 | WP_181576138 | LPD7 domain-containing protein | - |
| HVZ09_RS24255 (HVZ09_24210) | 82652..83203 | - | 552 | WP_000014584 | phospholipase D family protein | - |
| HVZ09_RS24260 (HVZ09_24215) | 83218..83508 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HVZ09_RS24265 (HVZ09_24220) | 83505..84653 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HVZ09_RS24270 (HVZ09_24225) | 84650..85468 | - | 819 | WP_000646097 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HVZ09_RS24275 (HVZ09_24230) | 85465..85923 | - | 459 | WP_001079808 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HVZ09_RS24280 (HVZ09_24235) | 86318..86902 | - | 585 | WP_000977526 | histidine phosphatase family protein | - |
| HVZ09_RS24285 (HVZ09_24240) | 86962..88164 | - | 1203 | WP_000976350 | conjugal transfer protein TraF | - |
| HVZ09_RS24290 (HVZ09_24245) | 88250..89074 | - | 825 | WP_001238943 | conjugal transfer protein TraE | traE |
| HVZ09_RS24295 (HVZ09_24250) | 89282..89407 | + | 126 | Protein_100 | transposase | - |
| HVZ09_RS24300 (HVZ09_24255) | 89464..90756 | - | 1293 | WP_181667537 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HVZ09_RS24305 (HVZ09_24260) | 90756..91412 | - | 657 | WP_001193549 | A24 family peptidase | - |
| HVZ09_RS24310 (HVZ09_24265) | 91397..91957 | - | 561 | WP_000014005 | lytic transglycosylase domain-containing protein | virB1 |
| HVZ09_RS24315 (HVZ09_24270) | 91967..92580 | - | 614 | Protein_104 | type 4 pilus major pilin | - |
| HVZ09_RS24320 (HVZ09_24275) | 92597..93682 | - | 1086 | WP_001208802 | type II secretion system F family protein | - |
| HVZ09_RS24325 (HVZ09_24280) | 93695..95248 | - | 1554 | WP_000362206 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HVZ09_RS24330 (HVZ09_24285) | 95259..95711 | - | 453 | WP_001247337 | type IV pilus biogenesis protein PilP | - |
| HVZ09_RS24335 (HVZ09_24290) | 95698..96993 | - | 1296 | WP_000752780 | type 4b pilus protein PilO2 | - |
| HVZ09_RS24340 (HVZ09_24295) | 96986..98668 | - | 1683 | WP_000748143 | PilN family type IVB pilus formation outer membrane protein | - |
| HVZ09_RS24345 (HVZ09_24300) | 98682..99119 | - | 438 | WP_000539807 | type IV pilus biogenesis protein PilM | - |
| HVZ09_RS24350 (HVZ09_24305) | 99119..100186 | - | 1068 | WP_042012078 | type IV pilus biogenesis lipoprotein PilL | - |
Host bacterium
| ID | 5740 | GenBank | NZ_CP057212 |
| Plasmid name | pRHB33-C07_3 | Incompatibility group | IncI1 |
| Plasmid size | 104967 bp | Coordinate of oriT [Strand] | 54368..54456 [-] |
| Host baterium | Escherichia fergusonii strain RHB33-C07 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |