Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 119863 |
| Name | oriT_pBD-50-Km_3  |
| Organism | Klebsiella michiganensis strain BD-50-Km |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP061933 (41147..41196 [+], 50 nt) |
| oriT length | 50 nt |
| IRs (inverted repeats) | 7..14, 17..24 (GCAAAATT..AATTTTGC) |
| Location of nic site | 33..34 |
| Conserved sequence flanking the nic site |
TGTGTGGTGA |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 50 nt
>oriT_pBD-50-Km_3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 14740 | GenBank | WP_228731170 |
| Name | traD_IE970_RS32515_pBD-50-Km_3 |
UniProt ID | _ |
| Length | 769 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 769 a.a. Molecular weight: 85608.74 Da Isoelectric Point: 5.3326
>WP_228731170.1 type IV conjugative transfer system coupling protein TraD [Klebsiella michiganensis]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGAGPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGTADTNSHAGEQPEPVSQPA
PAEVTVSPAPVKAPATTKMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNKDGVIEDMQAYDAWADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGAGPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGTADTNSHAGEQPEPVSQPA
PAEVTVSPAPVKAPATTKMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNKDGVIEDMQAYDAWADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 10359..38768
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| IE970_RS32515 (IE970_32520) | 10359..12668 | - | 2310 | WP_228731170 | type IV conjugative transfer system coupling protein TraD | virb4 |
| IE970_RS32520 (IE970_32525) | 12797..13486 | - | 690 | WP_023316411 | hypothetical protein | - |
| IE970_RS32525 (IE970_32530) | 13680..14414 | - | 735 | WP_116973176 | conjugal transfer complement resistance protein TraT | - |
| IE970_RS32530 (IE970_32535) | 14394..15362 | + | 969 | WP_094316038 | IS5 family transposase | - |
| IE970_RS32535 (IE970_32540) | 15453..16661 | + | 1209 | WP_029404400 | IS256 family transposase | - |
| IE970_RS32540 (IE970_32545) | 16652..16915 | - | 264 | WP_200519979 | hypothetical protein | - |
| IE970_RS32545 (IE970_32550) | 16921..19776 | - | 2856 | WP_195711721 | conjugal transfer mating-pair stabilization protein TraG | traG |
| IE970_RS32550 (IE970_32555) | 19776..21146 | - | 1371 | WP_200519980 | conjugal transfer pilus assembly protein TraH | traH |
| IE970_RS32555 (IE970_32560) | 21133..21561 | - | 429 | WP_101856563 | conjugal transfer protein TrbF | - |
| IE970_RS32560 (IE970_32565) | 21554..22120 | - | 567 | WP_101856562 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| IE970_RS32565 (IE970_32570) | 22095..22331 | - | 237 | WP_101856561 | type-F conjugative transfer system pilin chaperone TraQ | - |
| IE970_RS32570 (IE970_32575) | 22342..23094 | - | 753 | WP_064361002 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| IE970_RS32575 (IE970_32580) | 23117..23443 | - | 327 | WP_101856560 | hypothetical protein | - |
| IE970_RS32580 (IE970_32585) | 23669..23905 | - | 237 | WP_101856558 | conjugal transfer protein TrbE | - |
| IE970_RS32585 (IE970_32590) | 23895..24275 | - | 381 | WP_064360999 | hypothetical protein | - |
| IE970_RS32590 (IE970_32595) | 24429..24899 | - | 471 | WP_200519981 | hypothetical protein | - |
| IE970_RS32595 (IE970_32600) | 24983..26938 | - | 1956 | WP_200519983 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| IE970_RS32600 (IE970_32605) | 26938..27567 | - | 630 | WP_064349684 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| IE970_RS32605 (IE970_32610) | 27580..28569 | - | 990 | WP_064349687 | conjugal transfer pilus assembly protein TraU | traU |
| IE970_RS32610 (IE970_32615) | 28580..29209 | - | 630 | WP_064349689 | type-F conjugative transfer system protein TraW | traW |
| IE970_RS32615 (IE970_32620) | 29206..29598 | - | 393 | WP_064349691 | type-F conjugative transfer system protein TrbI | - |
| IE970_RS32620 (IE970_32625) | 29598..32237 | - | 2640 | WP_064349692 | type IV secretion system protein TraC | virb4 |
| IE970_RS32625 (IE970_32630) | 32322..32702 | - | 381 | WP_064349750 | hypothetical protein | - |
| IE970_RS32630 (IE970_32635) | 32717..33064 | - | 348 | WP_074180877 | hypothetical protein | - |
| IE970_RS32635 (IE970_32640) | 33061..33472 | - | 412 | Protein_33 | hypothetical protein | - |
| IE970_RS32640 (IE970_32645) | 33469..33690 | - | 222 | WP_064349696 | hypothetical protein | - |
| IE970_RS32645 (IE970_32650) | 33715..33930 | - | 216 | WP_064349698 | hypothetical protein | - |
| IE970_RS32650 (IE970_32655) | 34541..35110 | - | 570 | WP_195711726 | type IV conjugative transfer system lipoprotein TraV | traV |
| IE970_RS32655 (IE970_32660) | 35133..35741 | - | 609 | WP_200519985 | conjugal transfer pilus-stabilizing protein TraP | - |
| IE970_RS32660 (IE970_32665) | 35734..37155 | - | 1422 | WP_064349704 | F-type conjugal transfer pilus assembly protein TraB | traB |
| IE970_RS32665 (IE970_32670) | 37155..37892 | - | 738 | WP_064349705 | type-F conjugative transfer system secretin TraK | traK |
| IE970_RS32670 (IE970_32675) | 37879..38445 | - | 567 | WP_064349707 | type IV conjugative transfer system protein TraE | traE |
| IE970_RS32675 (IE970_32680) | 38463..38768 | - | 306 | WP_064349709 | type IV conjugative transfer system protein TraL | traL |
| IE970_RS32680 (IE970_32685) | 38782..39150 | - | 369 | WP_064349711 | type IV conjugative transfer system pilin TraA | - |
| IE970_RS32685 (IE970_32690) | 39219..39419 | - | 201 | WP_074180879 | TraY domain-containing protein | - |
| IE970_RS32690 (IE970_32695) | 39505..40209 | - | 705 | WP_064349713 | hypothetical protein | - |
| IE970_RS32695 (IE970_32700) | 40446..40838 | - | 393 | WP_064349715 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| IE970_RS32700 (IE970_32705) | 41271..41747 | + | 477 | WP_200519987 | transglycosylase SLT domain-containing protein | - |
| IE970_RS32705 (IE970_32710) | 41785..42315 | - | 531 | WP_200519989 | antirestriction protein | - |
Host bacterium
| ID | 20293 | GenBank | NZ_CP061933 |
| Plasmid name | pBD-50-Km_3 | Incompatibility group | IncFIB |
| Plasmid size | 135663 bp | Coordinate of oriT [Strand] | 41147..41196 [+] |
| Host baterium | Klebsiella michiganensis strain BD-50-Km |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | arsH, arsR, arsB, arsC |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |