Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 101676 |
| Name | oriT_p2018n8250667_1  |
| Organism | Escherichia coli strain COL3 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_JACYGB010000003 (93215..93567 [-], 353 nt) |
| oriT length | 353 nt |
| IRs (inverted repeats) | 256..263, 272..279 (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: 353 nt
>oriT_p2018n8250667_1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTCATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTCATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 1450 | GenBank | WP_001514237 |
| Name | traI_IYX22_RS23790_p2018n8250667_1 |
UniProt ID | A0A0F6X1E3 |
| Length | 1756 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1756 a.a. Molecular weight: 191942.70 Da Isoelectric Point: 5.7462
>WP_001514237.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Gammaproteobacteria]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAWLHTPAQQAIHLALPVVESKNLAFSMVDLLTEVKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPGSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPITAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREITGQERDRAAITEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMVREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHQEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAWLHTPAQQAIHLALPVVESKNLAFSMVDLLTEVKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPGSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPITAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREITGQERDRAAITEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 576 | GenBank | WP_001369361 |
| Name | WP_001369361_p2018n8250667_1 |
UniProt ID | B7LI64 |
| Length | 133 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 133 a.a. Molecular weight: 15409.70 Da Isoelectric Point: 9.9240
>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | B7LI64 |
| ID | 577 | GenBank | WP_001151524 |
| Name | WP_001151524_p2018n8250667_1 |
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 | 1125 | GenBank | WP_001514238 |
| Name | traD_IYX22_RS23795_p2018n8250667_1 |
UniProt ID | _ |
| Length | 717 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 717 a.a. Molecular weight: 81446.01 Da Isoelectric Point: 5.1693
>WP_001514238.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFKPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFKPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 68410..94138
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| IYX22_RS23795 | 68410..70563 | - | 2154 | WP_001514238 | type IV conjugative transfer system coupling protein TraD | virb4 |
| IYX22_RS23800 | 70816..71547 | - | 732 | WP_000850424 | conjugal transfer complement resistance protein TraT | - |
| IYX22_RS23805 | 71561..72070 | - | 510 | WP_000628099 | conjugal transfer entry exclusion protein TraS | - |
| IYX22_RS23810 | 72067..74892 | - | 2826 | WP_001007045 | conjugal transfer mating-pair stabilization protein TraG | traG |
| IYX22_RS23815 | 74889..76262 | - | 1374 | WP_001137358 | conjugal transfer pilus assembly protein TraH | traH |
| IYX22_RS23820 | 76262..76624 | - | 363 | WP_010379880 | P-type conjugative transfer protein TrbJ | - |
| IYX22_RS23825 | 76554..77099 | - | 546 | WP_000052618 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| IYX22_RS23830 | 77086..77370 | - | 285 | WP_000624110 | type-F conjugative transfer system pilin chaperone TraQ | - |
| IYX22_RS23835 | 77489..77836 | - | 348 | WP_001287677 | conjugal transfer protein TrbA | - |
| IYX22_RS23840 | 77852..78595 | - | 744 | WP_001514239 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| IYX22_RS23845 | 78588..78845 | - | 258 | WP_000864325 | conjugal transfer protein TrbE | - |
| IYX22_RS23850 | 78872..80680 | - | 1809 | WP_000821846 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| IYX22_RS23855 | 80677..81315 | - | 639 | WP_000777693 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| IYX22_RS23860 | 81324..82316 | - | 993 | WP_000830839 | conjugal transfer pilus assembly protein TraU | traU |
| IYX22_RS23865 | 82313..82945 | - | 633 | WP_001203720 | type-F conjugative transfer system protein TraW | traW |
| IYX22_RS23870 | 82942..83328 | - | 387 | WP_000214082 | type-F conjugative transfer system protein TrbI | - |
| IYX22_RS23875 | 83325..85952 | - | 2628 | Protein_78 | type IV secretion system protein TraC | - |
| IYX22_RS23880 | 86112..86333 | - | 222 | WP_001278689 | conjugal transfer protein TraR | - |
| IYX22_RS23885 | 86468..86983 | - | 516 | WP_000809841 | type IV conjugative transfer system lipoprotein TraV | traV |
| IYX22_RS23890 | 86980..87231 | - | 252 | WP_001038342 | conjugal transfer protein TrbG | - |
| IYX22_RS23895 | 87243..87440 | - | 198 | WP_001324648 | conjugal transfer protein TrbD | - |
| IYX22_RS23900 | 87427..88017 | - | 591 | WP_000002796 | conjugal transfer pilus-stabilizing protein TraP | - |
| IYX22_RS23905 | 88007..89434 | - | 1428 | WP_000146685 | F-type conjugal transfer pilus assembly protein TraB | traB |
| IYX22_RS23910 | 89434..90162 | - | 729 | WP_001230787 | type-F conjugative transfer system secretin TraK | traK |
| IYX22_RS23915 | 90149..90715 | - | 567 | WP_000399785 | type IV conjugative transfer system protein TraE | traE |
| IYX22_RS23920 | 90737..91048 | - | 312 | WP_187185589 | type IV conjugative transfer system protein TraL | traL |
| IYX22_RS23925 | 91063..91428 | - | 366 | WP_000994779 | type IV conjugative transfer system pilin TraA | - |
| IYX22_RS23930 | 91461..91856 | - | 396 | WP_001309237 | conjugal transfer relaxosome DNA-bindin protein TraY | - |
| IYX22_RS23935 | 91955..92644 | - | 690 | WP_000283385 | conjugal transfer transcriptional regulator TraJ | - |
| IYX22_RS23940 | 92831..93214 | - | 384 | WP_001151524 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| IYX22_RS23945 | 93629..94138 | + | 510 | WP_000759163 | transglycosylase SLT domain-containing protein | virB1 |
| IYX22_RS23950 | 94434..95255 | - | 822 | WP_001234468 | DUF932 domain-containing protein | - |
| IYX22_RS23955 | 95374..95661 | - | 288 | WP_000107520 | hypothetical protein | - |
| IYX22_RS23960 | 95962..96259 | + | 298 | Protein_95 | hypothetical protein | - |
| IYX22_RS23965 | 96560..96682 | - | 123 | WP_223195199 | Hok/Gef family protein | - |
| IYX22_RS24950 | 96627..96779 | - | 153 | Protein_97 | DUF5431 family protein | - |
| IYX22_RS23970 | 96930..97716 | - | 787 | Protein_98 | plasmid SOS inhibition protein A | - |
| IYX22_RS23975 | 97713..98147 | - | 435 | WP_000845922 | conjugation system SOS inhibitor PsiB | - |
Host bacterium
| ID | 2120 | GenBank | NZ_JACYGB010000003 |
| Plasmid name | p2018n8250667_1 | Incompatibility group | IncFII |
| Plasmid size | 136868 bp | Coordinate of oriT [Strand] | 93215..93567 [-] |
| Host baterium | Escherichia coli strain COL3 |
Cargo genes
| Drug resistance gene | blaTEM-1C, sitABCD |
| Virulence gene | iroB, iroC, iroD, iroE, iroN, iutA, iucC, iucB, iucA |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |