Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100614 |
| Name | oriT_pTF2  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_032100 (11061..11170 [-], 110 nt) |
| oriT length | 110 nt |
| IRs (inverted repeats) | IR1: 24..31, 35..42 (GTCGGGGC..GCCCTGAC) IR2: 49..65, 72..88 (GTAATTGTAATAGCGTC..GACGGTATTACAATTAC) |
| Location of nic site | 96..97 |
| Conserved sequence flanking the nic site |
CATCCTG|T |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 110 nt
>oriT_pTF2
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTCAGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 686 | GenBank | YP_009328544 |
| Name | NikB_pTF2 |
UniProt ID | A0A097SRB3 |
| Length | 899 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 899 a.a. Molecular weight: 104057.54 Da Isoelectric Point: 7.2601
>YP_009328544.1 NikB (plasmid) [Escherichia coli]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLYLIAPVLFERDPRMGFEPEGNDGQFNQVFAEMVAW
HNVTGFSEHGNYVITRPDVDQHREVSERGYRNYMDSNTYRDGTQPVQDSENRWEPPTPV
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPENRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLYLIAPVLFERDPRMGFEPEGNDGQFNQVFAEMVAW
HNVTGFSEHGNYVITRPDVDQHREVSERGYRNYMDSNTYRDGTQPVQDSENRWEPPTPV
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A097SRB3 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 22106..57713
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTE32_RS00105 (D616_p160022) | 18402..19037 | - | 636 | WP_072105541 | CPBP family intramembrane glutamic endopeptidase | - |
| HTE32_RS00110 | 19085..19351 | + | 267 | WP_172685524 | hypothetical protein | - |
| HTE32_RS00115 (D616_p160025) | 19822..22113 | - | 2292 | WP_072105542 | F-type conjugative transfer protein TrbC | - |
| HTE32_RS00120 (D616_p160026) | 22106..23176 | - | 1071 | WP_047088495 | IncI1-type conjugal transfer protein TrbB | trbB |
| HTE32_RS00125 (D616_p160027) | 23195..24403 | - | 1209 | WP_000121273 | IncI1-type conjugal transfer protein TrbA | trbA |
| HTE32_RS00130 (D616_p160029) | 24695..24847 | + | 153 | WP_001303307 | Hok/Gef family protein | - |
| HTE32_RS00135 (D616_p160030) | 24919..25170 | - | 252 | WP_001291965 | hypothetical protein | - |
| HTE32_RS00535 | 25669..25764 | + | 96 | WP_001303310 | DinQ-like type I toxin DqlB | - |
| HTE32_RS00140 (D616_p160031) | 25829..26113 | - | 285 | WP_001707309 | hypothetical protein | - |
| HTE32_RS00145 | 26397..26606 | + | 210 | WP_000062603 | HEAT repeat domain-containing protein | - |
| HTE32_RS00150 (D616_p160032) | 26678..27352 | - | 675 | WP_223866377 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HTE32_RS00155 (D616_p160033) | 27402..29570 | - | 2169 | WP_000698357 | DotA/TraY family protein | traY |
| HTE32_RS00160 (D616_p160034) | 29667..30251 | - | 585 | WP_001037987 | IncI1-type conjugal transfer protein TraX | - |
| HTE32_RS00165 (D616_p160035) | 30280..31482 | - | 1203 | WP_072105543 | IncI1-type conjugal transfer protein TraW | traW |
| HTE32_RS00170 (D616_p160036) | 31449..32063 | - | 615 | WP_000337399 | IncI1-type conjugal transfer protein TraV | traV |
| HTE32_RS00175 (D616_p160037) | 32063..35107 | - | 3045 | WP_032072194 | IncI1-type conjugal transfer protein TraU | traU |
| HTE32_RS00180 (D616_p160038) | 35197..35997 | - | 801 | WP_001164788 | IncI1-type conjugal transfer protein TraT | traT |
| HTE32_RS00185 (D616_p160039) | 35981..36169 | - | 189 | WP_001277255 | putative conjugal transfer protein TraS | - |
| HTE32_RS00190 (D616_p160040) | 36233..36637 | - | 405 | WP_001422824 | IncI1-type conjugal transfer protein TraR | traR |
| HTE32_RS00195 (D616_p160041) | 36688..37215 | - | 528 | WP_001055569 | conjugal transfer protein TraQ | traQ |
| HTE32_RS00200 (D616_p160042) | 37215..37919 | - | 705 | WP_032072195 | IncI1-type conjugal transfer protein TraP | traP |
| HTE32_RS00205 (D616_p160043) | 37919..39208 | - | 1290 | WP_032072196 | conjugal transfer protein TraO | traO |
| HTE32_RS00210 (D616_p160044) | 39211..40194 | - | 984 | WP_001191879 | IncI1-type conjugal transfer protein TraN | traN |
| HTE32_RS00215 (D616_p160045) | 40205..40897 | - | 693 | WP_000138552 | DotI/IcmL family type IV secretion protein | traM |
| HTE32_RS00220 (D616_p160046) | 40894..41241 | - | 348 | WP_001055900 | conjugal transfer protein | traL |
| HTE32_RS00225 (D616_p160047) | 41259..45026 | - | 3768 | WP_072105548 | LPD7 domain-containing protein | - |
| HTE32_RS00230 (D616_p160049) | 45116..45667 | - | 552 | WP_022630639 | phospholipase D family protein | - |
| HTE32_RS00235 (D616_p160050) | 45682..45972 | - | 291 | WP_001299214 | hypothetical protein | traK |
| HTE32_RS00240 (D616_p160051) | 45969..47117 | - | 1149 | WP_001024972 | plasmid transfer ATPase TraJ | virB11 |
| HTE32_RS00245 (D616_p160052) | 47114..47932 | - | 819 | WP_000866663 | IncI1-type conjugal transfer lipoprotein TraI | traI |
| HTE32_RS00250 (D616_p160053) | 47929..48387 | - | 459 | WP_022630640 | IncI1-type conjugal transfer lipoprotein TraH | - |
| HTE32_RS00255 (D616_p160054) | 48782..49366 | - | 585 | WP_032072199 | histidine phosphatase family protein | - |
| HTE32_RS00260 (D616_p160055) | 49426..50628 | - | 1203 | WP_000976350 | conjugal transfer protein TraF | - |
| HTE32_RS00265 (D616_p160056) | 50714..51538 | - | 825 | WP_021565538 | conjugal transfer protein TraE | traE |
| HTE32_RS00270 | 51746..51871 | + | 126 | Protein_54 | transposase | - |
| HTE32_RS00275 (D616_p160057) | 51928..53220 | - | 1293 | WP_001350014 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HTE32_RS00280 (D616_p160058) | 53220..53876 | - | 657 | WP_001193549 | A24 family peptidase | - |
| HTE32_RS00285 (D616_p160059) | 53861..54421 | - | 561 | WP_072105544 | lytic transglycosylase domain-containing protein | virB1 |
| HTE32_RS00290 (D616_p160060) | 54431..55045 | - | 615 | WP_032072200 | type 4 pilus major pilin | - |
| HTE32_RS00295 (D616_p160061) | 55062..56147 | - | 1086 | WP_001208802 | type II secretion system F family protein | - |
| HTE32_RS00300 (D616_p160062) | 56160..57713 | - | 1554 | WP_000362206 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HTE32_RS00305 (D616_p160063) | 57724..58176 | - | 453 | WP_001247337 | type IV pilus biogenesis protein PilP | - |
| HTE32_RS00310 | 58163..59296 | - | 1134 | Protein_62 | type 4b pilus protein PilO2 | - |
| HTE32_RS00315 (D616_p160064) | 59382..59807 | + | 426 | WP_000422741 | transposase | - |
| HTE32_RS00320 (D616_p160065) | 59804..60154 | + | 351 | WP_000624722 | IS66 family insertion sequence element accessory protein TnpB | - |
| HTE32_RS00325 (D616_p160066) | 60185..61798 | + | 1614 | WP_000080200 | IS66-like element ISEc23 family transposase | - |
| HTE32_RS00330 | 61828..61998 | - | 171 | Protein_66 | pilus assembly protein PilO | - |
Host bacterium
| ID | 1074 | GenBank | NC_032100 |
| Plasmid name | pTF2 | Incompatibility group | IncI1 |
| Plasmid size | 93112 bp | Coordinate of oriT [Strand] | 11061..11170 [-] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | blaCTX-M-1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |