Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 104529 |
| Name | oriT_SWHIN_107|unnamed3  |
| Organism | Shigella flexneri strain SWHIN_107 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP055102 (13655..13707 [-], 53 nt) |
| oriT length | 53 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 53 nt
>oriT_SWHIN_107|unnamed3
CACACGATTGTAACATGACCGGAACGGTCTTGTGTACAATCGGTATCGTGCCT
CACACGATTGTAACATGACCGGAACGGTCTTGTGTACAATCGGTATCGTGCCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 3206 | GenBank | WP_039022943 |
| Name | t4cp2_HUZ84_RS25035_SWHIN_107|unnamed3 |
UniProt ID | _ |
| Length | 652 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 652 a.a. Molecular weight: 73293.90 Da Isoelectric Point: 9.1581
>WP_039022943.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MDAKKTGGLILFLLLLLVGVLIASNYLGGYTALRYSSVDMSLLKWDTFHSVISTFSGNPQYKKLVFMAWF
GFSVPLIFFAIFMLIVVIGIMPKKVIYGDARLATDMDLSKSGFFPDKKSPYKHPPILIGKMFKGRYKKQF
IYFAGQQFLILYAPTRSGKGVGIVIPNCVNYPGSMVILDIKLENWFLSAGFRQKELGQKCFLFAPAGYAE
TIDQAIKGQICSHRWNPLDCVSRSDLLRETDLAKIAAILIPASDDPIWSDSARNLFVGLGLYLLDKERFH
LEQKAKGHNVPDVLVSISAILKTSVPDGGKDLAAWMGQEIENRSWISDKTKSFFFKFMSAPDRTRGSIET
NFSSPLSIFSNPITAEATNFSDFDIRDIRKKPMSIYLGLTPDALITHEKIVNLFFSLLVNENCRELPEHN
PDLKYQCLILLDEFTSMGKSEVIERAVGFTAGYNLRFMFILQNEGQGQKSDMYGQEGWTTFTENSAVVLY
YPPKSKNALAKKISEEIGVRDMKISKRSISSGGGKGGSSRTRNDDVIERPVLLPEEIVSLRDKKNKARNI
AIREIITSEFSRPFIANKIIWFEEPEFKRRVDIARNNHVDIPNLFTQEVMDEIAKIAEIYLPKAGGKKVM
VAGGNVITNPDLDNHDKTDVSE
MDAKKTGGLILFLLLLLVGVLIASNYLGGYTALRYSSVDMSLLKWDTFHSVISTFSGNPQYKKLVFMAWF
GFSVPLIFFAIFMLIVVIGIMPKKVIYGDARLATDMDLSKSGFFPDKKSPYKHPPILIGKMFKGRYKKQF
IYFAGQQFLILYAPTRSGKGVGIVIPNCVNYPGSMVILDIKLENWFLSAGFRQKELGQKCFLFAPAGYAE
TIDQAIKGQICSHRWNPLDCVSRSDLLRETDLAKIAAILIPASDDPIWSDSARNLFVGLGLYLLDKERFH
LEQKAKGHNVPDVLVSISAILKTSVPDGGKDLAAWMGQEIENRSWISDKTKSFFFKFMSAPDRTRGSIET
NFSSPLSIFSNPITAEATNFSDFDIRDIRKKPMSIYLGLTPDALITHEKIVNLFFSLLVNENCRELPEHN
PDLKYQCLILLDEFTSMGKSEVIERAVGFTAGYNLRFMFILQNEGQGQKSDMYGQEGWTTFTENSAVVLY
YPPKSKNALAKKISEEIGVRDMKISKRSISSGGGKGGSSRTRNDDVIERPVLLPEEIVSLRDKKNKARNI
AIREIITSEFSRPFIANKIIWFEEPEFKRRVDIARNNHVDIPNLFTQEVMDEIAKIAEIYLPKAGGKKVM
VAGGNVITNPDLDNHDKTDVSE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 30168..53703
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HUZ84_RS24970 (HUZ84_24755) | 25513..26045 | - | 533 | Protein_33 | thermonuclease family protein | - |
| HUZ84_RS24975 (HUZ84_24760) | 26075..26728 | - | 654 | WP_183121777 | hypothetical protein | - |
| HUZ84_RS24980 (HUZ84_24765) | 26740..27864 | - | 1125 | WP_000486719 | site-specific integrase | - |
| HUZ84_RS24985 (HUZ84_24770) | 28230..29516 | - | 1287 | WP_015057162 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HUZ84_RS24990 (HUZ84_24775) | 29529..30164 | - | 636 | WP_000934979 | A24 family peptidase | - |
| HUZ84_RS24995 (HUZ84_24780) | 30168..30650 | - | 483 | WP_001258095 | lytic transglycosylase domain-containing protein | virB1 |
| HUZ84_RS25000 (HUZ84_24785) | 30716..31273 | - | 558 | WP_000095048 | type 4 pilus major pilin | - |
| HUZ84_RS25005 (HUZ84_24790) | 31318..32427 | - | 1110 | WP_000974903 | type II secretion system F family protein | - |
| HUZ84_RS25010 (HUZ84_24795) | 32418..33956 | - | 1539 | WP_000466225 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HUZ84_RS25015 (HUZ84_24800) | 33981..34475 | - | 495 | WP_000912553 | type IV pilus biogenesis protein PilP | - |
| HUZ84_RS25020 (HUZ84_24805) | 34459..35769 | - | 1311 | WP_001454111 | type 4b pilus protein PilO2 | - |
| HUZ84_RS25025 (HUZ84_24810) | 35820..37463 | - | 1644 | WP_001035589 | PilN family type IVB pilus formation outer membrane protein | - |
| HUZ84_RS25030 (HUZ84_24815) | 37456..37992 | - | 537 | WP_001220543 | sigma 54-interacting transcriptional regulator | virb4 |
| HUZ84_RS25035 (HUZ84_24820) | 38039..39997 | - | 1959 | WP_039022943 | type IV secretory system conjugative DNA transfer family protein | - |
| HUZ84_RS25040 (HUZ84_24825) | 40013..41068 | - | 1056 | WP_001542006 | P-type DNA transfer ATPase VirB11 | virB11 |
| HUZ84_RS25045 (HUZ84_24830) | 41087..42226 | - | 1140 | WP_001542008 | TrbI/VirB10 family protein | virB10 |
| HUZ84_RS25050 (HUZ84_24835) | 42216..42917 | - | 702 | WP_049824867 | TrbG/VirB9 family P-type conjugative transfer protein | - |
| HUZ84_RS25055 (HUZ84_24840) | 42983..43717 | - | 735 | WP_000432282 | type IV secretion system protein | virB8 |
| HUZ84_RS25060 (HUZ84_24845) | 43883..46240 | - | 2358 | WP_039022942 | VirB4 family type IV secretion system protein | virb4 |
| HUZ84_RS25065 (HUZ84_24850) | 46246..46566 | - | 321 | WP_000362080 | VirB3 family type IV secretion system protein | virB3 |
| HUZ84_RS25070 | 46637..46927 | - | 291 | WP_000865479 | conjugal transfer protein | - |
| HUZ84_RS25075 (HUZ84_24860) | 46927..47511 | - | 585 | WP_001177114 | lytic transglycosylase domain-containing protein | virB1 |
| HUZ84_RS25080 (HUZ84_24865) | 47532..47930 | - | 399 | WP_001153669 | hypothetical protein | - |
| HUZ84_RS25085 (HUZ84_24870) | 48049..48486 | - | 438 | WP_000539665 | type IV pilus biogenesis protein PilM | - |
| HUZ84_RS25090 (HUZ84_24875) | 48492..49727 | - | 1236 | WP_039022941 | toxin co-regulated pilus biosynthesis Q family protein | - |
| HUZ84_RS25095 (HUZ84_24880) | 49730..50029 | - | 300 | WP_000835763 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HUZ84_RS25100 (HUZ84_24885) | 50096..50731 | - | 636 | WP_022645136 | hypothetical protein | - |
| HUZ84_RS25105 (HUZ84_24890) | 50779..51570 | + | 792 | WP_022645137 | DUF5710 domain-containing protein | - |
| HUZ84_RS25110 (HUZ84_24895) | 51825..52049 | - | 225 | WP_000713561 | EexN family lipoprotein | - |
| HUZ84_RS25115 (HUZ84_24900) | 52058..52702 | - | 645 | WP_001310442 | type IV secretion system protein | - |
| HUZ84_RS25120 (HUZ84_24905) | 52708..53703 | - | 996 | WP_001028541 | type IV secretion system protein | virB6 |
| HUZ84_RS25125 (HUZ84_24910) | 53707..53964 | - | 258 | WP_000739144 | hypothetical protein | - |
| HUZ84_RS25130 (HUZ84_24915) | 53961..54263 | - | 303 | WP_001360345 | hypothetical protein | - |
| HUZ84_RS25135 (HUZ84_24920) | 54534..54746 | - | 213 | WP_039022940 | hypothetical protein | - |
| HUZ84_RS25140 (HUZ84_24925) | 54757..54927 | - | 171 | WP_000550720 | hypothetical protein | - |
| HUZ84_RS25145 (HUZ84_24930) | 54931..55374 | - | 444 | WP_072037179 | NfeD family protein | - |
| HUZ84_RS25150 (HUZ84_24935) | 55748..56701 | - | 954 | WP_072109880 | SPFH domain-containing protein | - |
| HUZ84_RS25155 (HUZ84_24940) | 56728..56904 | - | 177 | WP_000753050 | hypothetical protein | - |
| HUZ84_RS25160 (HUZ84_24945) | 56897..57112 | - | 216 | WP_001127357 | DUF1187 family protein | - |
| HUZ84_RS25165 (HUZ84_24950) | 57105..57611 | - | 507 | WP_039022938 | CaiF/GrlA family transcriptional regulator | - |
Host bacterium
| ID | 4968 | GenBank | NZ_CP055102 |
| Plasmid name | SWHIN_107|unnamed3 | Incompatibility group | IncI2 |
| Plasmid size | 58696 bp | Coordinate of oriT [Strand] | 13655..13707 [-] |
| Host baterium | Shigella flexneri strain SWHIN_107 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |