Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100937 |
| Name | oriT_pMDR_56-3  |
| Organism | Escherichia coli strain MDR_56 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP019909 (2877..3338 [+], 462 nt) |
| oriT length | 462 nt |
| IRs (inverted repeats) | 142..151, 154..163 (ATAGGGTCGT..ACGACCCTAT) 231..238, 241..248 (GCAAAAAC..GTTTTTGC) |
| Location of nic site | 257..258 |
| Conserved sequence flanking the nic site |
GTGGGGTGT|GG |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 462 nt
>oriT_pMDR_56-3
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGGCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATGAAAATTGTCAGCACTGACCCTAACAAGGGTCGTCATAGGGTCGCTATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAGAACATAAACTAATGATTTAAAAAACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTACTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAATGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGATCTGCCATGCCACTGATTGCTTTGATCTTGCAGGCCGGGATTACAAAATAGATCCTGATTTACTGAGA
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGGCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATGAAAATTGTCAGCACTGACCCTAACAAGGGTCGTCATAGGGTCGCTATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAGAACATAAACTAATGATTTAAAAAACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTACTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAATGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGATCTGCCATGCCACTGATTGCTTTGATCTTGCAGGCCGGGATTACAAAATAGATCCTGATTTACTGAGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 1007 | GenBank | WP_078081141 |
| Name | TraI_pMDR_56-3 |
UniProt ID | _ |
| Length | 1756 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 1756 a.a. Molecular weight: 191879.62 Da Isoelectric Point: 6.0008
>WP_078081141.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 63321..84929
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| B1200_RS28615 (B1200_29385) | 62687..62914 | + | 228 | WP_000450520 | toxin-antitoxin system antitoxin VapB | - |
| B1200_RS28620 (B1200_29390) | 62914..63312 | + | 399 | WP_000911333 | tRNA(fMet)-specific endonuclease VapC | - |
| B1200_RS28625 (B1200_29395) | 63321..65474 | - | 2154 | WP_000009379 | type IV conjugative transfer system coupling protein TraD | virb4 |
| B1200_RS28630 (B1200_29400) | 65727..66458 | - | 732 | WP_000850416 | conjugal transfer complement resistance protein TraT | - |
| B1200_RS28635 (B1200_29405) | 66472..66981 | - | 510 | WP_000628105 | conjugal transfer entry exclusion protein TraS | - |
| B1200_RS28640 (B1200_29410) | 66978..69803 | - | 2826 | WP_001007036 | conjugal transfer mating-pair stabilization protein TraG | traG |
| B1200_RS28645 (B1200_29415) | 69800..71173 | - | 1374 | WP_000944319 | conjugal transfer pilus assembly protein TraH | traH |
| B1200_RS30940 | 71160..71552 | - | 393 | Protein_77 | F-type conjugal transfer protein TrbF | - |
| B1200_RS28660 (B1200_29430) | 71539..71880 | - | 342 | WP_001442101 | P-type conjugative transfer protein TrbJ | - |
| B1200_RS28665 (B1200_29435) | 71810..72355 | - | 546 | WP_000059833 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| B1200_RS28670 (B1200_29440) | 72342..72626 | - | 285 | WP_000624108 | type-F conjugative transfer system pilin chaperone TraQ | - |
| B1200_RS28675 (B1200_29445) | 72707..72982 | + | 276 | WP_001513501 | hypothetical protein | - |
| B1200_RS28680 (B1200_29450) | 72984..73331 | - | 348 | WP_001287907 | conjugal transfer protein TrbA | - |
| B1200_RS28685 (B1200_29455) | 73347..74090 | - | 744 | WP_001030378 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| B1200_RS28690 (B1200_29460) | 74083..74340 | - | 258 | WP_000864318 | conjugal transfer protein TrbE | - |
| B1200_RS28695 (B1200_29465) | 74367..76175 | - | 1809 | WP_078081142 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| B1200_RS28700 (B1200_29470) | 76172..76810 | - | 639 | WP_000777703 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| B1200_RS28705 (B1200_29475) | 76819..77811 | - | 993 | WP_000830183 | conjugal transfer pilus assembly protein TraU | traU |
| B1200_RS28710 (B1200_29480) | 77808..78440 | - | 633 | WP_001203720 | type-F conjugative transfer system protein TraW | traW |
| B1200_RS28715 (B1200_29485) | 78437..78823 | - | 387 | WP_000099688 | type-F conjugative transfer system protein TrbI | - |
| B1200_RS28720 (B1200_29490) | 78820..81447 | - | 2628 | WP_001064245 | type IV secretion system protein TraC | virb4 |
| B1200_RS28725 (B1200_29495) | 81607..81828 | - | 222 | WP_001278690 | conjugal transfer protein TraR | - |
| B1200_RS28730 (B1200_29500) | 81963..82478 | - | 516 | WP_000809838 | type IV conjugative transfer system lipoprotein TraV | traV |
| B1200_RS28735 (B1200_29505) | 82475..82726 | - | 252 | WP_001038351 | conjugal transfer protein TrbG | - |
| B1200_RS28740 (B1200_29510) | 82738..82935 | - | 198 | WP_001324648 | conjugal transfer protein TrbD | - |
| B1200_RS28745 (B1200_29515) | 82922..83512 | - | 591 | WP_000002787 | conjugal transfer pilus-stabilizing protein TraP | - |
| B1200_RS28750 (B1200_29520) | 83502..84929 | - | 1428 | WP_000146685 | F-type conjugal transfer pilus assembly protein TraB | traB |
Host bacterium
| ID | 1395 | GenBank | NZ_CP019909 |
| Plasmid name | pMDR_56-3 | Incompatibility group | IncFIC |
| Plasmid size | 85009 bp | Coordinate of oriT [Strand] | 2877..3338 [+] |
| Host baterium | Escherichia coli strain MDR_56 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |