Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200065 |
| Name | oriT_ICEVchBan9  |
| Organism | Vibrio cholerae MJ-1236 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | CP001485 (3060049..3060347 [-], 299 nt) |
| oriT length | 299 nt |
| IRs (inverted repeats) | 178..192, 216..230 (ATCGAGACGCCAAAC..GTTTGGCGTTTCGAT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | _ |
oriT sequence
Download Length: 299 nt
>oriT_ICEVchBan9
TTTCTACCAAACCAATTTCCCCATCCAATTAACCCCTAAAGCCAAAACCACTATCCGTTTGGCTTTTGGATCGAAACGCCAAACGTAAAACTGCCGTCACAATCACTGTTTGGCGTCTCGATATAAATCGACTCGCTCAATCCCATACCCGACAAGGGATACAGGCTGATTTCACTTAAAAACACCTAAAAAGACGTATCGCCATGAAGATACAAACCGTTTGGCAAGTTCAGGCCAGAATGCAAACGACGTTTGGCGTCTCAATTTTTTTGGCTAGGTCACCAGCCGCCAAACAGAGC
TTTCTACCAAACCAATTTCCCCATCCAATTAACCCCTAAAGCCAAAACCACTATCCGTTTGGCTTTTGGATCGAAACGCCAAACGTAAAACTGCCGTCACAATCACTGTTTGGCGTCTCGATATAAATCGACTCGCTCAATCCCATACCCGACAAGGGATACAGGCTGATTTCACTTAAAAACACCTAAAAAGACGTATCGCCATGAAGATACAAACCGTTTGGCAAGTTCAGGCCAGAATGCAAACGACGTTTGGCGTCTCAATTTTTTTGGCTAGGTCACCAGCCGCCAAACAGAGC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Wozniak RA et al. (2009) Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet. 5(12):e1000786. [PMID:20041216]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 2962770..3016244
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| VCD_003660 | 2958347..2959936 | - | 1590 | ACQ61816 | peptide chain release factor 3 | - |
| VCD_003661 | 2960193..2960840 | - | 648 | ACQ61817 | HTH-type transcriptional regulator for conjugative element SXT | - |
| VCD_003662 | 2960958..2961209 | + | 252 | ACQ61818 | uncharacterized protein conserved in bacteria prophage-related | - |
| VCD_003663 | 2961265..2962134 | + | 870 | ACQ61819 | hypothetical protein | - |
| VCD_003664 | 2962055..2962783 | + | 729 | ACQ61820 | hypothetical protein | - |
| VCD_003665 | 2962770..2963318 | + | 549 | ACQ61821 | soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) | virB1 |
| VCD_003666 | 2963315..2963614 | + | 300 | ACQ61822 | hypothetical protein | - |
| VCD_003667 | 2964666..2968235 | - | 3570 | ACQ61823 | IncF plasmid conjugative transfer protein TraG | traG |
| VCD_003668 | 2968239..2969627 | - | 1389 | ACQ61824 | IncF plasmid conjugative transfer pilus assembly protein TraH | traH |
| VCD_003669 | 2969630..2970574 | - | 945 | ACQ61825 | IncF plasmid conjugative transfer pilus assembly protein TraF | traF |
| VCD_003670 | 2970831..2971790 | - | 960 | ACQ61826 | integron integrase | - |
| VCD_003671 | 2972078..2972551 | + | 474 | ACQ61827 | dihydrofolate reductase | - |
| VCD_003672 | 2973754..2974122 | + | 369 | ACQ61828 | hypothetical protein | - |
| VCD_003673 | 2974222..2974923 | + | 702 | ACQ61829 | hypothetical protein | - |
| VCD_003674 | 2975596..2976303 | - | 708 | ACQ61830 | hypothetical protein | - |
| VCD_003675 | 2976393..2977466 | - | 1074 | ACQ61831 | hypothetical protein | - |
| VCD_003676 | 2977557..2977898 | - | 342 | ACQ61832 | hypothetical protein | - |
| VCD_003677 | 2977898..2978395 | - | 498 | ACQ61833 | DNA repair protein RadC | - |
| VCD_003678 | 2978480..2980135 | - | 1656 | ACQ61834 | hypothetical protein | - |
| VCD_003679 | 2980205..2980645 | - | 441 | ACQ61835 | hypothetical protein | - |
| VCD_003680 | 2980707..2981660 | - | 954 | ACQ61836 | cobalamine biosynthesis protein | - |
| VCD_003681 | 2981759..2982529 | - | 771 | ACQ61837 | hypothetical protein | - |
| VCD_003682 | 2982526..2983602 | - | 1077 | ACQ61838 | ATPase associated with various cellular activities AAA_5 | - |
| VCD_003683 | 2983695..2984711 | - | 1017 | ACQ61839 | DNA recombination protein | - |
| VCD_003684 | 2984772..2984915 | - | 144 | ACQ61840 | hypothetical protein | - |
| VCD_003685 | 2984997..2985815 | - | 819 | ACQ61841 | hypothetical protein | - |
| VCD_003686 | 2985895..2986314 | - | 420 | ACQ61842 | single-stranded DNA-binding protein | - |
| VCD_003687 | 2986330..2986668 | - | 339 | ACQ61843 | hypothetical protein | - |
| VCD_003688 | 2987024..2987626 | + | 603 | ACQ61844 | hypothetical protein | - |
| VCD_003689 | 2987717..2988379 | - | 663 | ACQ61845 | hypothetical protein | - |
| VCD_003690 | 2988410..2988883 | - | 474 | ACQ61846 | hypothetical protein | - |
| VCD_003691 | 2988974..2992615 | - | 3642 | ACQ61847 | IncF plasmid conjugative transfer protein TraN | traN |
| VCD_003692 | 2992669..2993703 | - | 1035 | ACQ61848 | IncF plasmid conjugative transfer pilus assembly protein TraU | traU |
| VCD_003693 | 2993681..2994844 | - | 1164 | ACQ61849 | hypothetical protein | traW |
| VCD_003694 | 2994816..2995328 | - | 513 | ACQ61850 | signal peptidase I | - |
| VCD_003695 | 2995312..2995659 | - | 348 | ACQ61851 | hypothetical protein | - |
| VCD_003696 | 2995652..2998069 | - | 2418 | ACQ61852 | IncF plasmid conjugative transfer pilus assembly protein TraC | virb4 |
| VCD_003697 | 2998051..2998743 | - | 693 | ACQ61853 | thiol:disulfide interchange protein DsbC | trbB |
| VCD_003698 | 2998888..3000333 | - | 1446 | ACQ61854 | type 4 fimbriae expression regulatory protein pilR | - |
| VCD_003699 | 3000336..3001871 | - | 1536 | ACQ61855 | hypothetical protein | - |
| VCD_003700 | 3001881..3002990 | - | 1110 | ACQ61856 | hypothetical protein | - |
| VCD_003701 | 3002987..3005716 | - | 2730 | ACQ61857 | hypothetical protein | - |
| VCD_003702 | 3006281..3007231 | - | 951 | ACQ61858 | Ync | - |
| VCD_003703 | 3007212..3008045 | - | 834 | ACQ61859 | Ynd | - |
| VCD_003704 | 3008223..3008609 | - | 387 | ACQ61860 | TraA | - |
| VCD_003705 | 3008606..3009256 | - | 651 | ACQ61861 | conjugative transfer protein TraV | traV |
| VCD_003706 | 3009253..3010545 | - | 1293 | ACQ61862 | IncF plasmid conjugative transfer pilus assembly protein TraB | traB |
| VCD_003707 | 3010542..3011444 | - | 903 | ACQ61863 | IncF plasmid conjugative transfer pilus assembly protein TraK | traK |
| VCD_003708 | 3011425..3012051 | - | 627 | ACQ61864 | hypothetical protein | traE |
| VCD_003709 | 3012048..3012335 | - | 288 | ACQ61865 | IncF plasmid conjugative transfer pilus assembly protein TraL | traL |
| VCD_003710 | 3012585..3013205 | + | 621 | ACQ61866 | hypothetical protein | - |
| VCD_003711 | 3013232..3013876 | - | 645 | ACQ61867 | conjugative transfer protein s043 | tfc7 |
| VCD_003712 | 3013854..3014390 | - | 537 | ACQ61868 | hypothetical protein | - |
| VCD_003713 | 3014424..3016244 | - | 1821 | ACQ61869 | TraD | virb4 |
| VCD_003714 | 3016293..3018443 | - | 2151 | ACQ61870 | TraI | - |
Region 2: 2988974..3016244
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| VCD_003684 | 2984772..2984915 | - | 144 | ACQ61840 | hypothetical protein | - |
| VCD_003685 | 2984997..2985815 | - | 819 | ACQ61841 | hypothetical protein | - |
| VCD_003686 | 2985895..2986314 | - | 420 | ACQ61842 | single-stranded DNA-binding protein | - |
| VCD_003687 | 2986330..2986668 | - | 339 | ACQ61843 | hypothetical protein | - |
| VCD_003688 | 2987024..2987626 | + | 603 | ACQ61844 | hypothetical protein | - |
| VCD_003689 | 2987717..2988379 | - | 663 | ACQ61845 | hypothetical protein | - |
| VCD_003690 | 2988410..2988883 | - | 474 | ACQ61846 | hypothetical protein | - |
| VCD_003691 | 2988974..2992615 | - | 3642 | ACQ61847 | IncF plasmid conjugative transfer protein TraN | traN |
| VCD_003692 | 2992669..2993703 | - | 1035 | ACQ61848 | IncF plasmid conjugative transfer pilus assembly protein TraU | traU |
| VCD_003693 | 2993681..2994844 | - | 1164 | ACQ61849 | hypothetical protein | traW |
| VCD_003694 | 2994816..2995328 | - | 513 | ACQ61850 | signal peptidase I | - |
| VCD_003695 | 2995312..2995659 | - | 348 | ACQ61851 | hypothetical protein | - |
| VCD_003696 | 2995652..2998069 | - | 2418 | ACQ61852 | IncF plasmid conjugative transfer pilus assembly protein TraC | virb4 |
| VCD_003697 | 2998051..2998743 | - | 693 | ACQ61853 | thiol:disulfide interchange protein DsbC | trbB |
| VCD_003698 | 2998888..3000333 | - | 1446 | ACQ61854 | type 4 fimbriae expression regulatory protein pilR | - |
| VCD_003699 | 3000336..3001871 | - | 1536 | ACQ61855 | hypothetical protein | - |
| VCD_003700 | 3001881..3002990 | - | 1110 | ACQ61856 | hypothetical protein | - |
| VCD_003701 | 3002987..3005716 | - | 2730 | ACQ61857 | hypothetical protein | - |
| VCD_003702 | 3006281..3007231 | - | 951 | ACQ61858 | Ync | - |
| VCD_003703 | 3007212..3008045 | - | 834 | ACQ61859 | Ynd | - |
| VCD_003704 | 3008223..3008609 | - | 387 | ACQ61860 | TraA | - |
| VCD_003705 | 3008606..3009256 | - | 651 | ACQ61861 | conjugative transfer protein TraV | traV |
| VCD_003706 | 3009253..3010545 | - | 1293 | ACQ61862 | IncF plasmid conjugative transfer pilus assembly protein TraB | traB |
| VCD_003707 | 3010542..3011444 | - | 903 | ACQ61863 | IncF plasmid conjugative transfer pilus assembly protein TraK | traK |
| VCD_003708 | 3011425..3012051 | - | 627 | ACQ61864 | hypothetical protein | traE |
| VCD_003709 | 3012048..3012335 | - | 288 | ACQ61865 | IncF plasmid conjugative transfer pilus assembly protein TraL | traL |
| VCD_003710 | 3012585..3013205 | + | 621 | ACQ61866 | hypothetical protein | - |
| VCD_003711 | 3013232..3013876 | - | 645 | ACQ61867 | conjugative transfer protein s043 | tfc7 |
| VCD_003712 | 3013854..3014390 | - | 537 | ACQ61868 | hypothetical protein | - |
| VCD_003713 | 3014424..3016244 | - | 1821 | ACQ61869 | TraD | virb4 |
| VCD_003714 | 3016293..3018443 | - | 2151 | ACQ61870 | TraI | - |
Host bacterium
| ID | 73 | Element type | |
| Element name | ICEVchBan9 | GenBank | CP001485 |
| Element size | 3149584 bp | Coordinate of oriT [Strand] | 3060049..3060347 [-] |
| Host bacterium | Vibrio cholerae MJ-1236 |
Cargo genes
| Drug resistance gene | dfrA1, sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |