Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 101558 |
| Name | oriT_EC-28|unnamed1  |
| Organism | Escherichia coli strain EC-28 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_JAWLTU010000002 (101981..102332 [-], 352 nt) |
| oriT length | 352 nt |
| IRs (inverted repeats) | 255..262, 271..278 (ACCGCTAG..CTAGCGGT) 192..198, 206..212 (TATAAAA..TTTTATA) 40..47, 50..57 (GCAAAAAC..GTTTTTGC) 4..11, 16..23 (TTGGTGGT..ACCACCAA) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 352 nt
>oriT_EC-28|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 1381 | GenBank | WP_284565373 |
| Name | traI_V6E60_RS24600_EC-28|unnamed1 |
UniProt ID | _ |
| Length | 1706 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1706 a.a. Molecular weight: 186712.93 Da Isoelectric Point: 5.9554
>WP_284565373.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIRETVGEDASLKSRDVAALDTRKSKQHVDPEIKMTEWMQT
LKETGFDIRAYRDAAEQRAYTRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
AGVIERARAGIDEAISREQLIPLDREKGMFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELAMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKYAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVEKALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRE
TERRADEIVRKMAENKPDLPDGKTELAVRDIAGQERDRTATSERETALPESVLRESQREREAVREVAREN
LLQRLLQQMERDMVRDLQKEKTLGGD
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIRETVGEDASLKSRDVAALDTRKSKQHVDPEIKMTEWMQT
LKETGFDIRAYRDAAEQRAYTRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
AGVIERARAGIDEAISREQLIPLDREKGMFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELAMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKYAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVEKALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRE
TERRADEIVRKMAENKPDLPDGKTELAVRDIAGQERDRTATSERETALPESVLRESQREREAVREVAREN
LLQRLLQQMERDMVRDLQKEKTLGGD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 499 | GenBank | WP_001309237 |
| Name | WP_001309237_EC-28|unnamed1 |
UniProt ID | A0A5W1N5T0 |
| Length | 131 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 131 a.a. Molecular weight: 15183.38 Da Isoelectric Point: 9.9240
>WP_001309237.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A5W1N5T0 |
| ID | 500 | GenBank | WP_001151524 |
| Name | WP_001151524_EC-28|unnamed1 |
UniProt ID | A0A5W2DT22 |
| Length | 127 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 127 a.a. Molecular weight: 14517.48 Da Isoelectric Point: 5.0516
>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A5W2DT22 |
T4CP
| ID | 1013 | GenBank | WP_040110343 |
| Name | traD_V6E60_RS24605_EC-28|unnamed1 |
UniProt ID | _ |
| Length | 729 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 729 a.a. Molecular weight: 82928.56 Da Isoelectric Point: 5.1119
>WP_040110343.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDDKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
KRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRKRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQIASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
TQQQMQRREEVNINVHRERGEDVEPGDDF
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDDKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
KRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRKRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQIASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPD
TQQQMQRREEVNINVHRERGEDVEPGDDF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 73931..102903
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| V6E60_RS24605 | 73931..76120 | - | 2190 | WP_040110343 | type IV conjugative transfer system coupling protein TraD | virb4 |
| V6E60_RS24610 | 76372..77103 | - | 732 | WP_000850424 | conjugal transfer complement resistance protein TraT | - |
| V6E60_RS24615 | 77117..77626 | - | 510 | WP_000628100 | conjugal transfer entry exclusion protein TraS | - |
| V6E60_RS24620 | 77623..80448 | - | 2826 | WP_001553826 | conjugal transfer mating-pair stabilization protein TraG | traG |
| V6E60_RS24625 | 80445..81818 | - | 1374 | WP_021518370 | conjugal transfer pilus assembly protein TraH | traH |
| V6E60_RS24630 | 81805..82197 | - | 393 | WP_000164675 | F-type conjugal transfer protein TrbF | - |
| V6E60_RS24635 | 82151..82465 | - | 315 | WP_023149603 | P-type conjugative transfer protein TrbJ | - |
| V6E60_RS24640 | 82455..83009 | - | 555 | WP_001553830 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| V6E60_RS24645 | 82996..83280 | - | 285 | WP_000624105 | type-F conjugative transfer system pilin chaperone TraQ | - |
| V6E60_RS24650 | 83361..83696 | + | 336 | WP_000415571 | hypothetical protein | - |
| V6E60_RS24655 | 83677..84018 | - | 342 | WP_000556794 | conjugal transfer protein TrbA | - |
| V6E60_RS24660 | 84032..84775 | - | 744 | WP_001030378 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| V6E60_RS24665 | 84768..85025 | - | 258 | WP_000864312 | conjugal transfer protein TrbE | - |
| V6E60_RS24670 | 85052..86860 | - | 1809 | WP_000821840 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| V6E60_RS24675 | 86857..87495 | - | 639 | WP_021518374 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| V6E60_RS24680 | 87504..88496 | - | 993 | WP_000830180 | conjugal transfer pilus assembly protein TraU | traU |
| V6E60_RS24685 | 88493..89125 | - | 633 | WP_001203720 | type-F conjugative transfer system protein TraW | traW |
| V6E60_RS24690 | 89122..89508 | - | 387 | WP_000099686 | type-F conjugative transfer system protein TrbI | - |
| V6E60_RS24695 | 89505..90608 | - | 1104 | Protein_105 | type IV secretion system protein TraC | - |
| V6E60_RS24700 | 90804..92345 | + | 1542 | WP_001298859 | IS21-like element ISEc12 family transposase | - |
| V6E60_RS24705 | 92360..93106 | + | 747 | WP_001016257 | IS21-like element ISEc12 family helper ATPase IstB | - |
| V6E60_RS24710 | 93183..94718 | - | 1536 | Protein_108 | TraC family protein | - |
| V6E60_RS24715 | 94878..95099 | - | 222 | WP_001278689 | conjugal transfer protein TraR | - |
| V6E60_RS24720 | 95234..95749 | - | 516 | WP_000809838 | type IV conjugative transfer system lipoprotein TraV | traV |
| V6E60_RS24725 | 95746..95997 | - | 252 | WP_001038342 | conjugal transfer protein TrbG | - |
| V6E60_RS24730 | 96009..96206 | - | 198 | WP_001324648 | conjugal transfer protein TrbD | - |
| V6E60_RS24735 | 96193..96783 | - | 591 | WP_000002787 | conjugal transfer pilus-stabilizing protein TraP | - |
| V6E60_RS24740 | 96773..98200 | - | 1428 | WP_000146685 | F-type conjugal transfer pilus assembly protein TraB | traB |
| V6E60_RS24745 | 98200..98928 | - | 729 | WP_001230787 | type-F conjugative transfer system secretin TraK | traK |
| V6E60_RS24750 | 98915..99481 | - | 567 | WP_000399792 | type IV conjugative transfer system protein TraE | traE |
| V6E60_RS24755 | 99503..99814 | - | 312 | WP_000012106 | type IV conjugative transfer system protein TraL | traL |
| V6E60_RS24760 | 99829..100194 | - | 366 | WP_000994779 | type IV conjugative transfer system pilin TraA | - |
| V6E60_RS24765 | 100227..100622 | - | 396 | WP_001309237 | conjugal transfer relaxosome DNA-bindin protein TraY | - |
| V6E60_RS24770 | 100721..101410 | - | 690 | WP_000283385 | conjugal transfer transcriptional regulator TraJ | - |
| V6E60_RS24775 | 101597..101980 | - | 384 | WP_001151524 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| V6E60_RS24780 | 102313..102903 | + | 591 | WP_192849409 | transglycosylase SLT domain-containing protein | virB1 |
| V6E60_RS24785 | 103200..104021 | - | 822 | WP_001234426 | DUF932 domain-containing protein | - |
| V6E60_RS24790 | 104139..104426 | - | 288 | WP_000107535 | hypothetical protein | - |
| V6E60_RS24795 | 104451..104657 | - | 207 | WP_000547968 | hypothetical protein | - |
| V6E60_RS24800 | 104727..104899 | + | 173 | Protein_126 | hypothetical protein | - |
| V6E60_RS24805 | 105628..107295 | + | 1668 | WP_012372796 | group II intron reverse transcriptase/maturase | - |
| V6E60_RS24810 | 107608..107799 | - | 192 | WP_001027495 | hypothetical protein | - |
Host bacterium
| ID | 2002 | GenBank | NZ_JAWLTU010000002 |
| Plasmid name | EC-28|unnamed1 | Incompatibility group | IncFIB |
| Plasmid size | 141891 bp | Coordinate of oriT [Strand] | 101981..102332 [-] |
| Host baterium | Escherichia coli strain EC-28 |
Cargo genes
| Drug resistance gene | mph(A), blaNDM-5, sul1, qacE, aadA2, dfrA12, tet(A), blaOXA-1, aac(6')-Ib-cr, blaCTX-M-15, sitABCD |
| Virulence gene | iutA, iucC, iucB, iucA |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |