Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100280 |
| Name | oriT_plasmid_59kb  |
| Organism | Yersinia pseudotuberculosis IP 31758 |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NC_009704 (50515..50597 [+], 83 nt) |
| oriT length | 83 nt |
| IRs (inverted repeats) | 1..19, 22..40 (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC) |
| Location of nic site | 48..49 |
| Conserved sequence flanking the nic site |
TATCTTG|C |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 83 nt
>oriT_plasmid_59kb
GTGAAGATAGATAACCGGCTTGCCGGTTAGCTAACTTCACCTATCTTGCCCTGTTTTAACCCCGTTTAACGCCAAGAGAGTAT
GTGAAGATAGATAACCGGCTTGCCGGTTAGCTAACTTCACCTATCTTGCCCTGTTTTAACCCCGTTTAACGCCAAGAGAGTAT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 351 | GenBank | WP_011988462 |
| Name | TraI_plasmid_59kb |
UniProt ID | A0A0U1QTA9 |
| Length | 873 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 873 a.a. Molecular weight: 97939.17 Da Isoelectric Point: 10.7619
>WP_011988462.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Yersinia pseudotuberculosis complex]
MIIRHIPMKSVKRSSYSGLTKYITNEQGKQERVGDINITNCNSEDVDWAINEIQATQKLNTRATGDKTYH
LFISFPAGESPSADILKDIEARVCSSIGYGEHQRVSAVHHDTDNLHIHISINKIHPSKHTLHEPYRAYST
FGDIAGKLEIEHGLQQTNHTAKKVGAENRAHDMEHHAGVESLLSWVKRECLESIRNSKSWGELHQVIQNN
GLELRESGNGLIITDQQGIAVKASSVSRDISKGKLEVKLGKFEKPQPQNKRSPKNNIGHSKRPRVGKVGQ
QPPPRSRHRFHRLGNIDSIDIDNGPRYKKEPIRMKANTTELYAKYKAEQSNVSAIRTAQWVAARNKKNRA
IEAAKRTGRLKRAAIKLLNGKGVNKKALYSLTSRTVKIDVEKAKAEYLKERKVIYEKCRRQAWADWLKSN
ATEGNKEALSALRSRESRQKLKGNTVTGKQADKNNSTPISDITPDNITKTGTVIYRVGDSAIRDDGDSLK
VSRGASQDGLEAALHMAIKRYGENISVNGSDEFKEKIVQAAVKAKLNIKFDDTDLELRRQFVMSQQATKE
QTHDSRTDSRTTNRSSIRTIATRGTRGASIRKRESGGRNARDIKPYTRSVGRTPPPEKTHNLRNLSELDM
VQHTNRSEVLLPSYVSSNVEQQGTKSNDGMRWGVRRARGVIHKRRSIDDKSRDIRPQVARVGKAPPPNSQ
NKWRHLSQLNNLELDLKAIRPLVARVGTTPPPLSQNRLRSLSELRKVELAQGVKKIQPPVNKSPLADFIP
QKVISTLSTGQVAADKYVNEREAKRGKGFDIVKHYRYNDYKGGASFAGIRQIDSESLALLKCDDHVIVMP
VEAATVRRLKRLSIGDEVIVTEKGVIKTKGRSR
MIIRHIPMKSVKRSSYSGLTKYITNEQGKQERVGDINITNCNSEDVDWAINEIQATQKLNTRATGDKTYH
LFISFPAGESPSADILKDIEARVCSSIGYGEHQRVSAVHHDTDNLHIHISINKIHPSKHTLHEPYRAYST
FGDIAGKLEIEHGLQQTNHTAKKVGAENRAHDMEHHAGVESLLSWVKRECLESIRNSKSWGELHQVIQNN
GLELRESGNGLIITDQQGIAVKASSVSRDISKGKLEVKLGKFEKPQPQNKRSPKNNIGHSKRPRVGKVGQ
QPPPRSRHRFHRLGNIDSIDIDNGPRYKKEPIRMKANTTELYAKYKAEQSNVSAIRTAQWVAARNKKNRA
IEAAKRTGRLKRAAIKLLNGKGVNKKALYSLTSRTVKIDVEKAKAEYLKERKVIYEKCRRQAWADWLKSN
ATEGNKEALSALRSRESRQKLKGNTVTGKQADKNNSTPISDITPDNITKTGTVIYRVGDSAIRDDGDSLK
VSRGASQDGLEAALHMAIKRYGENISVNGSDEFKEKIVQAAVKAKLNIKFDDTDLELRRQFVMSQQATKE
QTHDSRTDSRTTNRSSIRTIATRGTRGASIRKRESGGRNARDIKPYTRSVGRTPPPEKTHNLRNLSELDM
VQHTNRSEVLLPSYVSSNVEQQGTKSNDGMRWGVRRARGVIHKRRSIDDKSRDIRPQVARVGKAPPPNSQ
NKWRHLSQLNNLELDLKAIRPLVARVGTTPPPLSQNRLRSLSELRKVELAQGVKKIQPPVNKSPLADFIP
QKVISTLSTGQVAADKYVNEREAKRGKGFDIVKHYRYNDYKGGASFAGIRQIDSESLALLKCDDHVIVMP
VEAATVRRLKRLSIGDEVIVTEKGVIKTKGRSR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A0U1QTA9 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 6161..29492
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| YPSIP31758_RS00010 (YpsIP31758_A0042) | 1836..2138 | - | 303 | WP_011988449 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| YPSIP31758_RS00015 (YpsIP31758_A0043) | 2126..2416 | - | 291 | WP_011988472 | CopG family transcriptional regulator | - |
| YPSIP31758_RS24175 | 3122..3289 | - | 168 | WP_166485334 | hypothetical protein | - |
| YPSIP31758_RS00020 (YpsIP31758_A0044) | 3354..3548 | - | 195 | WP_041175615 | hypothetical protein | - |
| YPSIP31758_RS22360 (YpsIP31758_A0045) | 3928..4839 | - | 912 | WP_011988417 | zeta toxin family protein | - |
| YPSIP31758_RS00030 | 4836..5057 | - | 222 | WP_041175616 | hypothetical protein | - |
| YPSIP31758_RS00035 (YpsIP31758_A0046) | 5634..6002 | + | 369 | WP_011988477 | transcriptional regulator | - |
| YPSIP31758_RS00040 (YpsIP31758_A0047) | 6161..7120 | + | 960 | WP_041175630 | P-type conjugative transfer ATPase TrbB | virB11 |
| YPSIP31758_RS00045 (YpsIP31758_A0048) | 7133..7513 | + | 381 | WP_011988438 | TrbC/VirB2 family protein | virB2 |
| YPSIP31758_RS00050 (YpsIP31758_A0049) | 7516..7830 | + | 315 | WP_011988450 | conjugal transfer protein TrbD | virB3 |
| YPSIP31758_RS00055 (YpsIP31758_A0050) | 7823..10360 | + | 2538 | WP_011988420 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| YPSIP31758_RS00060 (YpsIP31758_A0051) | 10357..11079 | + | 723 | WP_011988424 | conjugal transfer protein TrbF | virB8 |
| YPSIP31758_RS00065 (YpsIP31758_A0052) | 11094..11981 | + | 888 | WP_011988419 | P-type conjugative transfer protein TrbG | virB9 |
| YPSIP31758_RS00070 (YpsIP31758_A0053) | 11984..12433 | + | 450 | WP_011988468 | conjugal transfer protein TrbH | - |
| YPSIP31758_RS00075 (YpsIP31758_A0054) | 12438..13817 | + | 1380 | WP_011988463 | TrbI/VirB10 family protein | virB10 |
| YPSIP31758_RS00080 (YpsIP31758_A0055) | 13835..14611 | + | 777 | WP_011988458 | P-type conjugative transfer protein TrbJ | virB5 |
| YPSIP31758_RS00085 | 14626..14826 | + | 201 | WP_041175617 | entry exclusion lipoprotein TrbK | - |
| YPSIP31758_RS00090 (YpsIP31758_A0056) | 14774..16195 | + | 1422 | WP_011988447 | P-type conjugative transfer protein TrbL | virB6 |
| YPSIP31758_RS00095 (YpsIP31758_A0057) | 16248..16868 | + | 621 | WP_011988436 | conjugal transfer protein TrbN | - |
| YPSIP31758_RS22365 (YpsIP31758_A0058) | 16987..17466 | + | 480 | WP_011988473 | transcription termination/antitermination NusG family protein | - |
| YPSIP31758_RS00105 (YpsIP31758_A0059) | 17489..18421 | + | 933 | WP_011988422 | TcpQ domain-containing protein | - |
| YPSIP31758_RS00110 (YpsIP31758_A0060) | 18434..20140 | + | 1707 | WP_011988414 | PilN family type IVB pilus formation outer membrane protein | - |
| YPSIP31758_RS00115 (YpsIP31758_A0061) | 20150..21484 | + | 1335 | WP_011988426 | type 4b pilus protein PilO2 | - |
| YPSIP31758_RS00120 (YpsIP31758_A0062) | 21471..21914 | + | 444 | WP_011988448 | type IV pilus biogenesis protein PilP | - |
| YPSIP31758_RS00125 (YpsIP31758_A0063) | 21911..23443 | + | 1533 | WP_011988476 | ATPase, T2SS/T4P/T4SS family | virB11 |
| YPSIP31758_RS00130 (YpsIP31758_A0064) | 23436..24500 | + | 1065 | WP_011988432 | type II secretion system F family protein | - |
| YPSIP31758_RS00135 (YpsIP31758_A0065) | 24517..25023 | + | 507 | WP_011988430 | type 4 pilus major pilin | - |
| YPSIP31758_RS00140 (YpsIP31758_A0066) | 25039..25992 | + | 954 | WP_011988446 | ATPase, T2SS/T4P/T4SS family | virB11 |
| YPSIP31758_RS00145 (YpsIP31758_A0001) | 26005..27261 | + | 1257 | WP_011988423 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| YPSIP31758_RS00150 (YpsIP31758_A0002) | 27495..27896 | + | 402 | WP_011988421 | hypothetical protein | - |
| YPSIP31758_RS00155 (YpsIP31758_A0003) | 27901..28332 | + | 432 | WP_011988469 | type IV pilus biogenesis protein PilM | - |
| YPSIP31758_RS00160 (YpsIP31758_A0004) | 28344..28967 | + | 624 | WP_011988455 | hypothetical protein | - |
| YPSIP31758_RS00165 (YpsIP31758_A0005) | 28986..29492 | + | 507 | WP_011988434 | lytic transglycosylase domain-containing protein | virB1 |
| YPSIP31758_RS00170 (YpsIP31758_A0006) | 29517..30002 | + | 486 | WP_011988460 | hypothetical protein | - |
| YPSIP31758_RS00175 (YpsIP31758_A0007) | 30036..30335 | + | 300 | WP_011988453 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| YPSIP31758_RS00180 (YpsIP31758_A0008) | 30468..30716 | + | 249 | WP_011988456 | hypothetical protein | - |
| YPSIP31758_RS00185 (YpsIP31758_A0009) | 30797..31144 | + | 348 | WP_011988418 | single-stranded DNA-binding protein | - |
| YPSIP31758_RS00190 | 31794..31994 | - | 201 | WP_041175619 | entry exclusion lipoprotein TrbK | - |
| YPSIP31758_RS00195 (YpsIP31758_A0010) | 32134..32799 | - | 666 | WP_011988445 | hypothetical protein | - |
| YPSIP31758_RS24180 (YpsIP31758_A0011) | 32812..32982 | - | 171 | WP_011988452 | hypothetical protein | - |
| YPSIP31758_RS00205 (YpsIP31758_A0012) | 33378..33923 | + | 546 | WP_011988474 | hypothetical protein | - |
Host bacterium
| ID | 742 | GenBank | NC_009704 |
| Plasmid name | pIP31758 | Incompatibility group | pIP31758(p59) |
| Plasmid size | 58679 bp | Coordinate of oriT [Strand] | 50515..50597 [+] |
| Host baterium | Yersinia pseudotuberculosis IP 31758 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |