Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 119623 |
| Name | oriT_RL316|unnamed  |
| Organism | Escherichia sp. RL316 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP141240 (52633..52705 [-], 73 nt) |
| oriT length | 73 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 73 nt
>oriT_RL316|unnamed
GTCGGGGCAAAGCCCTGACCAGGTGGGGAATGTCTGAGTGCGCGTGCGCGGTCCGACATTCCCACATCCTGTC
GTCGGGGCAAAGCCCTGACCAGGTGGGGAATGTCTGAGTGCGCGTGCGCGGTCCGACATTCCCACATCCTGTC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12400 | GenBank | WP_029391987 |
| Name | Relaxase_VJF96_RS00335_RL316|unnamed |
UniProt ID | A0A2H5C199 |
| Length | 906 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 906 a.a. Molecular weight: 105112.51 Da Isoelectric Point: 8.2682
>WP_029391987.1 MULTISPECIES: relaxase/mobilization nuclease domain-containing protein [Enterobacteriaceae]
MNAIIPHKRRDGRSSFEDLIAYTSVRDDVQENELTEDSEIKSDVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCNSLETAAEEMQYKADKAVFSRNDTDPVFHYILSWPAHESPRPEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINWLSWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPEMARNGELESCLDVHRTLAKAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGHSIGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
ALIQCRSQIEEMIAGGDFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAGADIFERVKPECRYNPELAASDEVEPGFRRDPVLRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQVRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAAQGDRAAVSQLRGWDYRDRRSRNKDKRRTTNADRCVVLCEPGGTPLFNNVAKLEARLQK
NGSVHFRDTRTGKNVCTDYGDRVVFYHHTDRNELAEKLDLIAPVLFSRNGKLGFEPEGSYQQFNDVFAEM
VAWHNAAGITGNGHFTITRPDVDLHRQRSEQYYREYIRQQTRLSESHDDNYTLRQEKTWEPPSPGM
MNAIIPHKRRDGRSSFEDLIAYTSVRDDVQENELTEDSEIKSDVPHRNRFRRLVDYATRLRNEKFVSLID
VMKDGSQWVNFYGVTCFHNCNSLETAAEEMQYKADKAVFSRNDTDPVFHYILSWPAHESPRPEQLFDCVR
HTLKSLELSKHQYVAAVHTDTDNLHVHVAVNRVHPETGYINWLSWSQEKLSRACRELELKHGFAPDNGCF
VHAPGNRIVRKTALVRERRNAWRRGKKQTFREYIAQMSIAGLREEPAQDWLSLHKRLASDGLYITMQEGE
LVVKDGWDRAREGVALSSFGPSWTAEKLGRKLGEYQPVPTDIFSQVGTPGRYDPEAINVDIRPEKVAETE
SLKQYACRHFAERLPEMARNGELESCLDVHRTLAKAGLWMGIQHGHLVLHDGFDKQQTPVRADSVWPLMT
LDYMQDLDGGWQPVPKDIFTQVIPGERFRGHSIGTQAVSDYEWYRMRMGTGPQGAIKRELFSDKESLWGY
ALIQCRSQIEEMIAGGDFSWQACHEMFARKGLMLQKQHHGLVIVDAFNHELTPVKASSIHPDLTLSRAEP
QAGPFEIAGADIFERVKPECRYNPELAASDEVEPGFRRDPVLRRERREARAAAREDLRARYLAWKEHWRK
PDLRYGERLREIHAACRRRKAYIRVQFRDPQVRKLHYHIAEVQRMQALIRLKESVKEERLSLIAEGKWYP
LSYRQWVEQQAAQGDRAAVSQLRGWDYRDRRSRNKDKRRTTNADRCVVLCEPGGTPLFNNVAKLEARLQK
NGSVHFRDTRTGKNVCTDYGDRVVFYHHTDRNELAEKLDLIAPVLFSRNGKLGFEPEGSYQQFNDVFAEM
VAWHNAAGITGNGHFTITRPDVDLHRQRSEQYYREYIRQQTRLSESHDDNYTLRQEKTWEPPSPGM
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A2H5C199 |
Auxiliary protein
| ID | 7056 | GenBank | WP_001291058 |
| Name | WP_001291058_RL316|unnamed |
UniProt ID | A0A7I0L241 |
| Length | 110 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 110 a.a. Molecular weight: 12730.52 Da Isoelectric Point: 9.9656
>WP_001291058.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSEKKTRTGSENRKRIVKFTARFTEDEAEIVREKAESSGQTVSTFIRSSSLDKVVNCRTDDRMIDEIMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITEYVNALRRDLMGR
MSEKKTRTGSENRKRIVKFTARFTEDEAEIVREKAESSGQTVSTFIRSSSLDKVVNCRTDDRMIDEIMRL
GRLQKHLFVEGKRTGDKEYAEVLVAITEYVNALRRDLMGR
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A7I0L241 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 60999..107208
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| VJF96_RS00340 | 56011..56406 | - | 396 | Protein_67 | conjugal transfer protein TrbC | - |
| VJF96_RS00345 | 56438..58009 | - | 1572 | WP_000381395 | IS66-like element ISCro1 family transposase | - |
| VJF96_RS00350 | 58029..58376 | - | 348 | WP_000624622 | IS66 family insertion sequence element accessory protein TnpB | - |
| VJF96_RS00355 | 58376..59053 | - | 678 | WP_001682408 | IS66-like element accessory protein TnpA | - |
| VJF96_RS00360 | 59117..61018 | - | 1902 | Protein_71 | F-type conjugative transfer protein TrbC | - |
| VJF96_RS00365 | 60999..62117 | - | 1119 | WP_029391999 | DsbC family protein | trbB |
| VJF96_RS00370 | 62114..63466 | - | 1353 | WP_065749868 | conjugal transfer protein TrbA | trbA |
| VJF96_RS00375 | 63777..63860 | + | 84 | WP_271298668 | DinQ-like type I toxin DqlB | - |
| VJF96_RS00380 | 63923..64099 | - | 177 | WP_032172741 | hypothetical protein | - |
| VJF96_RS00385 | 64250..64717 | - | 468 | WP_000598962 | thermonuclease family protein | - |
| VJF96_RS00390 | 64877..65500 | + | 624 | WP_001155252 | helix-turn-helix domain-containing protein | - |
| VJF96_RS00395 | 65698..65913 | - | 216 | WP_000266543 | hypothetical protein | - |
| VJF96_RS00400 | 65917..66285 | - | 369 | WP_029391948 | hypothetical protein | - |
| VJF96_RS00405 | 66584..66826 | - | 243 | WP_029391947 | hypothetical protein | - |
| VJF96_RS00410 | 66825..67010 | + | 186 | WP_024194018 | hypothetical protein | - |
| VJF96_RS00415 | 67155..67307 | + | 153 | WP_021532728 | Hok/Gef family protein | - |
| VJF96_RS00420 | 67304..67465 | - | 162 | WP_021580032 | hypothetical protein | - |
| VJF96_RS00425 | 67621..67752 | - | 132 | Protein_84 | ethanolamine utilization protein EutE | - |
| VJF96_RS00430 | 67847..68056 | + | 210 | WP_000062946 | HEAT repeat domain-containing protein | - |
| VJF96_RS00435 | 68121..68774 | - | 654 | WP_029391946 | plasmid IncI1-type surface exclusion protein ExcA | - |
| VJF96_RS00440 | 68862..71027 | - | 2166 | WP_029391945 | DotA/TraY family protein | traY |
| VJF96_RS00445 | 71100..71669 | - | 570 | WP_000650755 | conjugal transfer protein TraX | - |
| VJF96_RS00450 | 71666..72871 | - | 1206 | WP_029391944 | conjugal transfer protein TraW | traW |
| VJF96_RS00455 | 72832..73449 | - | 618 | WP_029391943 | hypothetical protein | traV |
| VJF96_RS00460 | 73449..76493 | - | 3045 | WP_029391942 | conjugal transfer protein | traU |
| VJF96_RS00465 | 76669..77049 | - | 381 | WP_000690886 | hypothetical protein | - |
| VJF96_RS00470 | 77049..77357 | - | 309 | WP_029391941 | hypothetical protein | - |
| VJF96_RS00475 | 77553..77870 | + | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| VJF96_RS00480 | 77867..78400 | - | 534 | WP_001221666 | lipocalin family protein | - |
| VJF96_RS00485 | 78494..79639 | - | 1146 | WP_000976514 | extended-spectrum class C beta-lactamase CMY-2 | - |
| VJF96_RS00490 | 79963..81225 | - | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| VJF96_RS00495 | 81322..81507 | - | 186 | WP_029394194 | hypothetical protein | - |
| VJF96_RS00500 | 81562..82380 | - | 819 | WP_072132149 | conjugal transfer protein TraT | traT |
| VJF96_RS00505 | 82295..82546 | - | 252 | WP_021532719 | hypothetical protein | - |
| VJF96_RS00510 | 82603..83001 | - | 399 | WP_029391936 | DUF6750 family protein | traR |
| VJF96_RS00515 | 83048..83578 | - | 531 | WP_000987022 | conjugal transfer protein TraQ | traQ |
| VJF96_RS00520 | 83575..84288 | - | 714 | WP_021532717 | conjugal transfer protein TraP | traP |
| VJF96_RS00525 | 84285..85616 | - | 1332 | WP_029391934 | conjugal transfer protein TraO | traO |
| VJF96_RS00530 | 85620..86594 | - | 975 | WP_029391933 | DotH/IcmK family type IV secretion protein | traN |
| VJF96_RS00535 | 86605..87300 | - | 696 | WP_029391932 | DotI/IcmL family type IV secretion protein | traM |
| VJF96_RS00540 | 87312..87662 | - | 351 | WP_021532713 | hypothetical protein | traL |
| VJF96_RS00545 | 87679..91740 | - | 4062 | WP_029391931 | LPD7 domain-containing protein | - |
| VJF96_RS00550 | 91804..92094 | - | 291 | WP_000817799 | hypothetical protein | traK |
| VJF96_RS00555 | 92091..93239 | - | 1149 | WP_000625247 | plasmid transfer ATPase TraJ | virB11 |
| VJF96_RS00560 | 93223..94059 | - | 837 | WP_029391930 | type IV secretory system conjugative DNA transfer family protein | traI |
| VJF96_RS00565 | 94056..94508 | - | 453 | WP_001081199 | DotD/TraH family lipoprotein | - |
| VJF96_RS00570 | 94746..94877 | + | 132 | WP_257792844 | hypothetical protein | - |
| VJF96_RS00575 | 94867..96069 | - | 1203 | WP_029391929 | conjugal transfer protein TraF | - |
| VJF96_RS00580 | 96159..96980 | - | 822 | WP_000804089 | hypothetical protein | traE |
| VJF96_RS00585 | 97231..97776 | - | 546 | WP_029391928 | hypothetical protein | - |
| VJF96_RS00590 | 97895..98176 | - | 282 | WP_029391927 | hypothetical protein | - |
| VJF96_RS00595 | 98217..99386 | - | 1170 | WP_029391926 | site-specific integrase | - |
| VJF96_RS00600 | 99710..100132 | - | 423 | WP_252347182 | hypothetical protein | - |
| VJF96_RS00605 | 100218..100601 | - | 384 | WP_236926536 | shufflon protein D' | - |
| VJF96_RS00610 | 101084..101473 | + | 390 | Protein_121 | phage tail protein | - |
| VJF96_RS00615 | 101478..102812 | - | 1335 | WP_059327959 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| VJF96_RS00620 | 102809..103516 | - | 708 | WP_202110611 | A24 family peptidase | - |
| VJF96_RS00625 | 103476..103952 | - | 477 | WP_029391914 | lytic transglycosylase domain-containing protein | virB1 |
| VJF96_RS00630 | 104011..104547 | - | 537 | WP_029391915 | type 4 pilus major pilin | - |
| VJF96_RS00635 | 104598..105698 | - | 1101 | WP_029391916 | type II secretion system F family protein | - |
| VJF96_RS00640 | 105700..107208 | - | 1509 | WP_021532701 | GspE/PulE family protein | virB11 |
| VJF96_RS00645 | 107305..107901 | - | 597 | WP_029391917 | hypothetical protein | - |
| VJF96_RS00650 | 107997..108551 | - | 555 | WP_021532699 | hypothetical protein | - |
| VJF96_RS00655 | 108600..109052 | - | 453 | WP_029391918 | type IV pilus biogenesis protein PilP | - |
| VJF96_RS00660 | 109042..110337 | - | 1296 | WP_021532697 | type 4b pilus protein PilO2 | - |
| VJF96_RS00665 | 110358..111977 | - | 1620 | WP_021532696 | PilN family type IVB pilus formation outer membrane protein | - |
Host bacterium
| ID | 20053 | GenBank | NZ_CP141240 |
| Plasmid name | RL316|unnamed | Incompatibility group | IncB/O/K/Z |
| Plasmid size | 117209 bp | Coordinate of oriT [Strand] | 52633..52705 [-] |
| Host baterium | Escherichia sp. RL316 |
Cargo genes
| Drug resistance gene | sul1, aac(3)-VIa, ant(3'')-Ia, blaCMY-2 |
| Virulence gene | htpB |
| Metal resistance gene | merR, merT, merP, merA, merD, merE |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |