Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 117991 |
| Name | oriT_pHDA2C.3  |
| Organism | Candidatus Hamiltonella defensa strain A2C |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP017609 (36394..36473 [-], 80 nt) |
| oriT length | 80 nt |
| IRs (inverted repeats) | 24..30, 33..39 (CGCTTGC..GCAAGCG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 80 nt
>oriT_pHDA2C.3
GGACAAGATATGTTTTGAAGCACCGCTTGCAAGCAAGCGTCCCTTCAAAACTCTTGGTCAGTGCTTCGCCCCGACACCCC
GGACAAGATATGTTTTGAAGCACCGCTTGCAAGCAAGCGTCCCTTCAAAACTCTTGGTCAGTGCTTCGCCCCGACACCCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 11412 | GenBank | WP_234811192 |
| Name | traI_BJP41_RS12400_pHDA2C.3 |
UniProt ID | _ |
| Length | 267 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 267 a.a. Molecular weight: 31598.12 Da Isoelectric Point: 9.5250
>WP_234811192.1 TraI/MobA(P) family conjugative relaxase [Candidatus Hamiltonella defensa]
MFESARHSLKALGMSDHQYVTAIHRDTDHLHCHVAANRIHPVTYKVADDAYDISKLHKASREMELKYGWT
RTHGCYVINDHHQVVRSYSHQKPMPIEAKKLEYYSDKESFYGYAVRECREEISKILGEKNLYWERLHAVL
IRAGLELKKKDRGLAIYDRVHPEQTPLKASSLHPQLTLSKLVPRLGEFESAPRVMEFKNEQWEVTLTNYM
VSSHYDDRLHLRDHQARMTRRLERAEAREELKLRYQHDKKKRNALLLTQKIVSELFP
MFESARHSLKALGMSDHQYVTAIHRDTDHLHCHVAANRIHPVTYKVADDAYDISKLHKASREMELKYGWT
RTHGCYVINDHHQVVRSYSHQKPMPIEAKKLEYYSDKESFYGYAVRECREEISKILGEKNLYWERLHAVL
IRAGLELKKKDRGLAIYDRVHPEQTPLKASSLHPQLTLSKLVPRLGEFESAPRVMEFKNEQWEVTLTNYM
VSSHYDDRLHLRDHQARMTRRLERAEAREELKLRYQHDKKKRNALLLTQKIVSELFP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 13337 | GenBank | WP_100103847 |
| Name | trbC_BJP41_RS11130_pHDA2C.3 |
UniProt ID | _ |
| Length | 709 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 709 a.a. Molecular weight: 79919.21 Da Isoelectric Point: 7.4644
>WP_100103847.1 F-type conjugative transfer protein TrbC [Candidatus Hamiltonella defensa]
MNKRPSSLDPHRINRPVFNPSLTDTVLSPTGVQWGFLIALVLGCLWPVTLLMGLPACVILLIIFCDRPFR
MPIRLPTDIGGPDLTTEQEGFKARKGGAGLFSFITRTRHCEQAAGILCLGYARGKSLARELWLNLDDALR
HIQLIATTGAGKTEAILSVYLNALCWGRGMCLSDGKAENKLAFAVLSLARRFGREDDVYVLNFLTAGNSK
FSDLMKDNKSRPQSNSINLFANASETFIIQLMDSLLPKVGSNENGWQEKAKAMIAALIYALCYKREKDGL
FLSQRVIQDYLPLRKIVELYQEAKKNHWHEEGYKPLEHYLNTLPGFDMALIDSPSEWSKTVWEQHGFLIQ
QFTRMLSLFNDIYGQVFPQGAGDIDLKDVLHNDRILVVLIPALELSNSEAATLGKLYISGLRMTLSQDLG
GQLEGKREDVLLSQKFAQQFPYPIIFDELGAYFASGIDKMAAQMRSLQYMLMIAAQDVQSMMDKSMREFL
TVSANQRTKWFMALEDAQDTFNLIRSAAGKGYYSELSSVKRKGSLSGSRYEDADTHHIRERDNIELTELK
ALNKGEGVILFQDAVVRSAAIFIPDEEKLSSKLPMRINRFIELKRPTFDALCEVVPELRHQGDSFKQEVN
GILKKLEQPPQKKARMEDKTLMAVATLALNLDNRNDLSYTPEERGILLFEAARHALKKTQGQYTMEKEPK
EIALEHSTP
MNKRPSSLDPHRINRPVFNPSLTDTVLSPTGVQWGFLIALVLGCLWPVTLLMGLPACVILLIIFCDRPFR
MPIRLPTDIGGPDLTTEQEGFKARKGGAGLFSFITRTRHCEQAAGILCLGYARGKSLARELWLNLDDALR
HIQLIATTGAGKTEAILSVYLNALCWGRGMCLSDGKAENKLAFAVLSLARRFGREDDVYVLNFLTAGNSK
FSDLMKDNKSRPQSNSINLFANASETFIIQLMDSLLPKVGSNENGWQEKAKAMIAALIYALCYKREKDGL
FLSQRVIQDYLPLRKIVELYQEAKKNHWHEEGYKPLEHYLNTLPGFDMALIDSPSEWSKTVWEQHGFLIQ
QFTRMLSLFNDIYGQVFPQGAGDIDLKDVLHNDRILVVLIPALELSNSEAATLGKLYISGLRMTLSQDLG
GQLEGKREDVLLSQKFAQQFPYPIIFDELGAYFASGIDKMAAQMRSLQYMLMIAAQDVQSMMDKSMREFL
TVSANQRTKWFMALEDAQDTFNLIRSAAGKGYYSELSSVKRKGSLSGSRYEDADTHHIRERDNIELTELK
ALNKGEGVILFQDAVVRSAAIFIPDEEKLSSKLPMRINRFIELKRPTFDALCEVVPELRHQGDSFKQEVN
GILKKLEQPPQKKARMEDKTLMAVATLALNLDNRNDLSYTPEERGILLFEAARHALKKTQGQYTMEKEPK
EIALEHSTP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 4755..29992
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| BJP41_RS10940 (BJP41_10540) | 1..597 | + | 597 | WP_234811177 | toxin co-regulated pilus biosynthesis Q family protein | - |
| BJP41_RS10945 (BJP41_10545) | 594..2276 | + | 1683 | WP_100103824 | PilN family type IVB pilus formation outer membrane protein | - |
| BJP41_RS10950 (BJP41_10550) | 2288..2626 | - | 339 | WP_100103825 | helix-turn-helix domain-containing protein | - |
| BJP41_RS10955 (BJP41_10555) | 2607..2987 | - | 381 | WP_100103826 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| BJP41_RS10960 (BJP41_10560) | 3051..4361 | + | 1311 | WP_100103827 | type 4b pilus protein PilO2 | - |
| BJP41_RS10965 (BJP41_10565) | 4348..4758 | + | 411 | WP_100103828 | type IV pilus biogenesis protein PilP | - |
| BJP41_RS10970 (BJP41_10570) | 4755..6302 | + | 1548 | WP_100103829 | GspE/PulE family protein | virB11 |
| BJP41_RS10975 (BJP41_10575) | 6289..7353 | + | 1065 | WP_100103830 | type II secretion system F family protein | - |
| BJP41_RS10980 (BJP41_10580) | 7365..7874 | + | 510 | WP_100103496 | type 4 pilus major pilin | - |
| BJP41_RS10985 (BJP41_10585) | 8127..9491 | + | 1365 | WP_100103831 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| BJP41_RS10990 (BJP41_10590) | 9543..9974 | + | 432 | WP_100103832 | type IV pilus biogenesis protein PilM | - |
| BJP41_RS10995 (BJP41_10595) | 9977..10597 | + | 621 | WP_193432766 | prepilin peptidase | - |
| BJP41_RS11000 (BJP41_10600) | 10640..11110 | + | 471 | WP_100103834 | lytic transglycosylase domain-containing protein | virB1 |
| BJP41_RS11005 (BJP41_10605) | 11165..11614 | + | 450 | WP_100103835 | DotD/TraH family lipoprotein | - |
| BJP41_RS11010 (BJP41_10610) | 11611..12426 | + | 816 | WP_100103836 | type IV secretion system DotC family protein | traI |
| BJP41_RS11015 (BJP41_10615) | 12413..13009 | + | 597 | Protein_15 | ATPase, T2SS/T4P/T4SS family | - |
| BJP41_RS11020 (BJP41_10620) | 13066..13443 | + | 378 | WP_012737971 | IS630 transposase-related protein | - |
| BJP41_RS11025 (BJP41_10625) | 13367..13888 | + | 522 | WP_320410290 | IS630 family transposase | - |
| BJP41_RS11030 (BJP41_10630) | 13971..14483 | + | 513 | WP_234811178 | ATPase, T2SS/T4P/T4SS family | - |
| BJP41_RS11035 (BJP41_10635) | 14545..14805 | + | 261 | WP_100103837 | IcmT/TraK family protein | traK |
| BJP41_RS11040 (BJP41_10640) | 14820..16985 | + | 2166 | WP_234811179 | LPD7 domain-containing protein | - |
| BJP41_RS12380 (BJP41_10645) | 16982..17554 | + | 573 | WP_234811181 | hypothetical protein | - |
| BJP41_RS11045 (BJP41_10650) | 17566..17997 | + | 432 | WP_100103838 | conjugal transfer protein TraL | traL |
| BJP41_RS11050 (BJP41_10655) | 18080..18694 | + | 615 | WP_234811183 | DotI/IcmL/TraM family protein | traM |
| BJP41_RS11055 (BJP41_10660) | 18733..19698 | + | 966 | WP_234811185 | DotH/IcmK family type IV secretion protein | traN |
| BJP41_RS11060 (BJP41_10665) | 19702..20874 | + | 1173 | WP_100103841 | conjugal transfer protein TraO | traO |
| BJP41_RS11065 (BJP41_10670) | 20871..21623 | + | 753 | WP_100103842 | conjugal transfer protein TraP | traP |
| BJP41_RS11070 (BJP41_10675) | 21637..22176 | + | 540 | WP_100096804 | conjugal transfer protein TraQ | traQ |
| BJP41_RS11075 (BJP41_10680) | 22234..22629 | + | 396 | WP_100103843 | DUF6750 family protein | traR |
| BJP41_RS11080 (BJP41_10685) | 22673..23368 | + | 696 | WP_193432912 | TraT conjugal transfer protein | traT |
| BJP41_RS12385 | 23365..24495 | + | 1131 | WP_234811187 | hypothetical protein | traU |
| BJP41_RS12390 | 24467..25378 | + | 912 | WP_234811189 | hypothetical protein | traU |
| BJP41_RS11090 (BJP41_10695) | 25394..25927 | - | 534 | WP_086934965 | IS630 family transposase | - |
| BJP41_RS11095 (BJP41_10700) | 25839..26216 | - | 378 | WP_234811160 | IS630 transposase-related protein | - |
| BJP41_RS11105 (BJP41_10705) | 26503..27138 | + | 636 | WP_100103844 | plasmid IncI1-type surface exclusion protein ExcA | - |
| BJP41_RS11110 (BJP41_10710) | 27161..27490 | - | 330 | WP_234811167 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| BJP41_RS11115 (BJP41_10715) | 27503..27772 | - | 270 | WP_044612608 | hypothetical protein | - |
| BJP41_RS11120 (BJP41_10720) | 27886..28980 | + | 1095 | WP_100103845 | conjugal transfer protein TrbA | trbA |
| BJP41_RS11125 (BJP41_10725) | 29099..29992 | + | 894 | WP_234811168 | DsbC family protein | trbB |
| BJP41_RS11130 (BJP41_10730) | 29985..32114 | + | 2130 | WP_100103847 | F-type conjugative transfer protein TrbC | - |
| BJP41_RS11135 (BJP41_10735) | 32121..32402 | - | 282 | WP_100103848 | ProQ/FINO family protein | - |
| BJP41_RS11140 (BJP41_10740) | 32690..33652 | - | 963 | WP_100103849 | Rpn family recombination-promoting nuclease/putative transposase | - |
| BJP41_RS11145 (BJP41_10745) | 33658..34014 | - | 357 | WP_100103850 | HU family DNA-binding protein | - |
| BJP41_RS12395 (BJP41_10750) | 34152..34811 | - | 660 | WP_234811169 | LPD7 domain-containing protein | - |
Host bacterium
| ID | 18424 | GenBank | NZ_CP017609 |
| Plasmid name | pHDA2C.3 | Incompatibility group | - |
| Plasmid size | 50279 bp | Coordinate of oriT [Strand] | 36394..36473 [-] |
| Host baterium | Candidatus Hamiltonella defensa strain A2C |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |