Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100593 |
| Name | oriT_pH1038-142  |
| Organism | Escherichia coli |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_025141 (38965..39613 [+], 649 nt) |
| oriT length | 649 nt |
| IRs (inverted repeats) | IR1: 198..207, 211..220 (ATTAGGTGTT..AATACCTAAT) IR2:319..324, 330..335 (AAAAAA..TTTTTT) IR3: 393..402, 405..414 (GTATTCATGC..GCATGAATAC) |
| Location of nic site | 301..302 |
| Conserved sequence flanking the nic site |
GGTGT|ATAGC |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 649 nt
>oriT_pH1038-142
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAACAAAAGATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTAGGTGTTTTTAATACCTAATTATTACCGAATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGATCTACGTAGGTTAAGGACTAACTGACTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACACTATTACAACAAAAGTACATCAAAATTACATCAAAAGTACATCACTTGAAGGTTGACAGTACAACAGAATTACATCATTATCTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAACAAAAGATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTAGGTGTTTTTAATACCTAATTATTACCGAATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTGTGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGATCTACGTAGGTTAAGGACTAACTGACTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACACTATTACAACAAAAGTACATCAAAATTACATCAAAAGTACATCACTTGAAGGTTGACAGTACAACAGAATTACATCATTATCTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 665 | GenBank | YP_009068536 |
| Name | TraI_pH1038-142 |
UniProt ID | I7EM40 |
| Length | 1078 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 1078 a.a. Molecular weight: 120126.36 Da Isoelectric Point: 6.5223
>YP_009068536.1 TraI (plasmid) [Escherichia coli]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAACALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLSGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAACALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | I7EM40 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 22214..38637
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTC81_RS00115 | 17488..17838 | + | 351 | Protein_23 | WbuC family cupin fold metalloprotein | - |
| HTC81_RS00120 (D616_p141028) | 17885..18760 | - | 876 | WP_013188473 | extended-spectrum class A beta-lactamase CTX-M-1 | - |
| HTC81_RS00125 (D616_p141029) | 18945..19127 | - | 183 | WP_031942424 | hypothetical protein | - |
| HTC81_RS00130 (D616_p141030) | 19118..19822 | + | 705 | WP_001067855 | IS6-like element IS26 family transposase | - |
| HTC81_RS00135 (D616_p141031) | 19884..20081 | - | 198 | WP_000844102 | hypothetical protein | - |
| HTC81_RS00140 (D616_p141032) | 20086..20727 | - | 642 | WP_001694850 | restriction endonuclease | - |
| HTC81_RS00145 (D616_p141033) | 20783..21016 | - | 234 | WP_001191790 | hypothetical protein | - |
| HTC81_RS00150 | 21130..21444 | - | 315 | WP_000734776 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HTC81_RS00155 (D616_p141035) | 21407..21784 | - | 378 | WP_000504251 | hypothetical protein | - |
| HTC81_RS00160 (D616_p141036) | 21800..22171 | - | 372 | WP_011867773 | H-NS family nucleoid-associated regulatory protein | - |
| HTC81_RS00165 (D616_p141037) | 22214..22948 | + | 735 | WP_000033783 | lytic transglycosylase domain-containing protein | virB1 |
| HTC81_RS00170 (D616_p141038) | 22957..23238 | + | 282 | WP_000440698 | transcriptional repressor KorA | - |
| HTC81_RS00175 (D616_p141039) | 23248..23541 | + | 294 | WP_000209137 | TrbC/VirB2 family protein | virB2 |
| HTC81_RS00180 (D616_p141040) | 23591..23908 | + | 318 | WP_000496058 | VirB3 family type IV secretion system protein | virB3 |
| HTC81_RS00185 (D616_p141041) | 23908..26508 | + | 2601 | WP_001200711 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HTC81_RS00190 (D616_p141042) | 26526..27239 | + | 714 | WP_000749362 | type IV secretion system protein | virB5 |
| HTC81_RS00195 (D616_p141043) | 27247..27474 | + | 228 | WP_000734973 | IncN-type entry exclusion lipoprotein EexN | - |
| HTC81_RS00200 (D616_p141044) | 27490..28530 | + | 1041 | WP_000886022 | type IV secretion system protein | virB6 |
| HTC81_RS00205 (D616_p141046) | 28749..29447 | + | 699 | WP_000646594 | type IV secretion system protein | virB8 |
| HTC81_RS00210 (D616_p141047) | 29458..30342 | + | 885 | WP_000735067 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HTC81_RS00215 (D616_p141048) | 30342..31502 | + | 1161 | WP_000101711 | type IV secretion system protein VirB10 | virB10 |
| HTC81_RS00220 (D616_p141049) | 31544..32539 | + | 996 | WP_000128596 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HTC81_RS00225 (D616_p141050) | 32539..33072 | + | 534 | WP_000731968 | phospholipase D family protein | - |
| HTC81_RS00230 (D616_p141051) | 33246..33872 | - | 627 | WP_000434930 | DUF6710 family protein | - |
| HTC81_RS00235 (D616_p141052) | 33872..37108 | - | 3237 | WP_015059325 | MobF family relaxase | - |
| HTC81_RS00240 (D616_p141053) | 37108..38637 | - | 1530 | WP_000342688 | type IV secretion system DNA-binding domain-containing protein | virb4 |
| HTC81_RS00245 (D616_p141054) | 38639..39055 | - | 417 | WP_001532083 | hypothetical protein | - |
| HTC81_RS00850 | 39568..39987 | + | 420 | WP_000802909 | plasmid stabilization protein StbA | - |
| HTC81_RS00255 (D616_p141057) | 39996..40712 | + | 717 | WP_000861577 | StbB family protein | - |
| HTC81_RS00260 (D616_p141058) | 40714..41082 | + | 369 | WP_000414913 | plasmid stabilization protein StbC | - |
| HTC81_RS00265 (D616_p141060) | 41265..41609 | + | 345 | WP_015059326 | hypothetical protein | - |
| HTC81_RS00270 (D616_p141061) | 41720..42040 | - | 321 | WP_000211833 | protein CcgAII | - |
| HTC81_RS00275 (D616_p141062) | 42095..42274 | - | 180 | WP_000214483 | protein CcgAI | - |
| HTC81_RS00280 (D616_p141064) | 43106..43615 | - | 510 | WP_000129958 | antirestriction protein ArdA | - |
Region 2: 79335..106034
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTC81_RS00465 (D616_p141118) | 75301..75735 | + | 435 | WP_000845901 | conjugation system SOS inhibitor PsiB | - |
| HTC81_RS00470 (D616_p141119) | 75732..76494 | + | 763 | Protein_96 | plasmid SOS inhibition protein A | - |
| HTC81_RS00865 | 76673..76822 | + | 150 | Protein_97 | plasmid maintenance protein Mok | - |
| HTC81_RS00475 (D616_p141121) | 76764..76889 | + | 126 | WP_001372321 | type I toxin-antitoxin system Hok family toxin | - |
| HTC81_RS00870 | 77109..77339 | + | 231 | WP_071587244 | hypothetical protein | - |
| HTC81_RS00875 | 77337..77510 | - | 174 | Protein_100 | hypothetical protein | - |
| HTC81_RS00480 (D616_p141126) | 77808..78096 | + | 289 | Protein_101 | hypothetical protein | - |
| HTC81_RS00485 (D616_p141127) | 78217..79038 | + | 822 | WP_001234469 | DUF932 domain-containing protein | - |
| HTC81_RS00490 (D616_p141130) | 79335..79982 | - | 648 | WP_000614936 | transglycosylase SLT domain-containing protein | virB1 |
| HTC81_RS00495 (D616_p141131) | 80259..80642 | + | 384 | WP_032072221 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| HTC81_RS00500 (D616_p141132) | 80833..81519 | + | 687 | WP_000332484 | PAS domain-containing protein | - |
| HTC81_RS00505 (D616_p141133) | 81613..81840 | + | 228 | WP_001254386 | conjugal transfer relaxosome protein TraY | - |
| HTC81_RS00510 (D616_p141134) | 81874..82233 | + | 360 | WP_000340272 | type IV conjugative transfer system pilin TraA | - |
| HTC81_RS00515 (D616_p141135) | 82248..82559 | + | 312 | WP_000012106 | type IV conjugative transfer system protein TraL | traL |
| HTC81_RS00520 (D616_p141136) | 82581..83147 | + | 567 | WP_000399792 | type IV conjugative transfer system protein TraE | traE |
| HTC81_RS00525 (D616_p141137) | 83134..83862 | + | 729 | WP_001230787 | type-F conjugative transfer system secretin TraK | traK |
| HTC81_RS00530 (D616_p141138) | 83862..85289 | + | 1428 | WP_000146668 | F-type conjugal transfer pilus assembly protein TraB | traB |
| HTC81_RS00535 (D616_p141139) | 85279..85851 | + | 573 | WP_024179131 | conjugal transfer pilus-stabilizing protein TraP | - |
| HTC81_RS00540 (D616_p141140) | 85848..86165 | + | 318 | WP_001057292 | conjugal transfer protein TrbD | virb4 |
| HTC81_RS00545 (D616_p141141) | 86162..86413 | + | 252 | WP_001038341 | conjugal transfer protein TrbG | - |
| HTC81_RS00550 (D616_p141142) | 86410..86925 | + | 516 | WP_000809902 | type IV conjugative transfer system lipoprotein TraV | traV |
| HTC81_RS00555 (D616_p141143) | 87060..87281 | + | 222 | WP_001278692 | conjugal transfer protein TraR | - |
| HTC81_RS00560 (D616_p141145) | 87441..90068 | + | 2628 | WP_032072222 | type IV secretion system protein TraC | virb4 |
| HTC81_RS00565 (D616_p141146) | 90065..90451 | + | 387 | WP_000214084 | type-F conjugative transfer system protein TrbI | - |
| HTC81_RS00570 (D616_p141147) | 90448..91080 | + | 633 | WP_001203746 | type-F conjugative transfer system protein TraW | traW |
| HTC81_RS00575 (D616_p141148) | 91077..92069 | + | 993 | WP_000830839 | conjugal transfer pilus assembly protein TraU | traU |
| HTC81_RS00580 (D616_p141149) | 92095..92556 | + | 462 | WP_000277845 | hypothetical protein | - |
| HTC81_RS00585 (D616_p141150) | 92586..93038 | + | 453 | WP_000069427 | hypothetical protein | - |
| HTC81_RS00590 (D616_p141151) | 93066..93704 | + | 639 | WP_001104248 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| HTC81_RS00595 (D616_p141152) | 93701..95509 | + | 1809 | WP_000821823 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| HTC81_RS00600 (D616_p141153) | 95536..95793 | + | 258 | WP_000864325 | conjugal transfer protein TrbE | - |
| HTC81_RS00605 (D616_p141154) | 95786..96529 | + | 744 | WP_001030376 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| HTC81_RS00610 (D616_p141155) | 96545..96892 | + | 348 | WP_001287893 | conjugal transfer protein TrbA | - |
| HTC81_RS00615 (D616_p141156) | 97011..97295 | + | 285 | WP_000624110 | type-F conjugative transfer system pilin chaperone TraQ | - |
| HTC81_RS00620 (D616_p141157) | 97282..97827 | + | 546 | WP_000052614 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| HTC81_RS00625 (D616_p141158) | 97757..98119 | + | 363 | WP_023181029 | P-type conjugative transfer protein TrbJ | - |
| HTC81_RS00630 (D616_p141159) | 98119..99492 | + | 1374 | WP_021530364 | conjugal transfer pilus assembly protein TraH | traH |
| HTC81_RS00635 (D616_p141160) | 99489..102314 | + | 2826 | WP_032072223 | conjugal transfer mating-pair stabilization protein TraG | traG |
| HTC81_RS00640 (D616_p141161) | 102311..102820 | + | 510 | WP_000628099 | conjugal transfer entry exclusion protein TraS | - |
| HTC81_RS00645 (D616_p141162) | 102834..103565 | + | 732 | WP_000850424 | conjugal transfer complement resistance protein TraT | - |
| HTC81_RS00650 (D616_p141164) | 103818..106034 | + | 2217 | WP_032072224 | type IV conjugative transfer system coupling protein TraD | virb4 |
Host bacterium
| ID | 1053 | GenBank | NC_025141 |
| Plasmid name | pH1038-142 | Incompatibility group | IncN |
| Plasmid size | 142875 bp | Coordinate of oriT [Strand] | 38965..39613 [+] |
| Host baterium | Escherichia coli |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | mercury resistance |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |