Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113566 |
| Name | oriT_pSH275-1  |
| Organism | Shigella sonnei strain SH275-1 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_MG299138 (15108..15160 [-], 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_pSH275-1
CACACGATTGTAACATGACCGGAACGGTCTTGTGTACAATCGGTATCGTGCCT
CACACGATTGTAACATGACCGGAACGGTCTTGTGTACAATCGGTATCGTGCCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 10052 | GenBank | WP_039022943 |
| Name | t4cp2_HPG28_RS00240_pSH275-1 |
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: 34422..58568
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HPG28_RS00175 | 29747..30400 | - | 654 | WP_170855322 | hypothetical protein | - |
| HPG28_RS00180 | 30412..31536 | - | 1125 | WP_000486716 | site-specific integrase | - |
| HPG28_RS00410 | 31599..31820 | + | 222 | Protein_38 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HPG28_RS00190 | 32484..33770 | - | 1287 | WP_015057162 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HPG28_RS00195 | 33783..34418 | - | 636 | WP_000934977 | A24 family peptidase | - |
| HPG28_RS00200 | 34422..34904 | - | 483 | WP_001258095 | lytic transglycosylase domain-containing protein | virB1 |
| HPG28_RS00205 | 34970..35527 | - | 558 | WP_000095048 | type 4 pilus major pilin | - |
| HPG28_RS00210 | 35572..36681 | - | 1110 | WP_000974903 | type II secretion system F family protein | - |
| HPG28_RS00215 | 36672..38210 | - | 1539 | WP_000466225 | GspE/PulE family protein | virB11 |
| HPG28_RS00220 | 38235..38729 | - | 495 | WP_000912553 | type IV pilus biogenesis protein PilP | - |
| HPG28_RS00225 | 38713..40035 | - | 1323 | WP_000454142 | type 4b pilus protein PilO2 | - |
| HPG28_RS00230 | 40074..41717 | - | 1644 | WP_001035590 | PilN family type IVB pilus formation outer membrane protein | - |
| HPG28_RS00235 | 41710..42234 | - | 525 | WP_001401691 | sigma 54-interacting transcriptional regulator | virb4 |
| HPG28_RS00240 | 42281..44239 | - | 1959 | WP_039022943 | type IV secretory system conjugative DNA transfer family protein | - |
| HPG28_RS00245 | 44255..45310 | - | 1056 | WP_001542006 | P-type DNA transfer ATPase VirB11 | virB11 |
| HPG28_RS00250 | 45329..46468 | - | 1140 | WP_001542008 | TrbI/VirB10 family protein | virB10 |
| HPG28_RS00255 | 46458..47159 | - | 702 | WP_049824867 | TrbG/VirB9 family P-type conjugative transfer protein | - |
| HPG28_RS00260 | 47225..47959 | - | 735 | WP_000432282 | virB8 family protein | virB8 |
| HPG28_RS00265 | 48125..50482 | - | 2358 | WP_065304451 | VirB4 family type IV secretion system protein | virb4 |
| HPG28_RS00270 | 50488..50808 | - | 321 | WP_000362080 | VirB3 family type IV secretion system protein | virB3 |
| HPG28_RS00405 | 50879..51169 | - | 291 | WP_000865479 | conjugal transfer protein | - |
| HPG28_RS00280 | 51169..51753 | - | 585 | WP_001177114 | lytic transglycosylase domain-containing protein | virB1 |
| HPG28_RS00285 | 51774..52172 | - | 399 | WP_001153669 | hypothetical protein | - |
| HPG28_RS00290 | 52291..52728 | - | 438 | WP_000539665 | type IV pilus biogenesis protein PilM | - |
| HPG28_RS00295 | 52734..53969 | - | 1236 | WP_015059538 | TcpQ domain-containing protein | - |
| HPG28_RS00300 | 53972..54271 | - | 300 | WP_000835764 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HPG28_RS00305 | 54339..54620 | - | 282 | WP_000638823 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| HPG28_RS00310 | 54610..54861 | - | 252 | WP_000121741 | type II toxin-antitoxin system Phd/YefM family antitoxin | - |
| HPG28_RS00315 | 54961..55596 | - | 636 | WP_022645136 | hypothetical protein | - |
| HPG28_RS00320 | 55644..56435 | + | 792 | WP_022645137 | DUF5710 domain-containing protein | - |
| HPG28_RS00325 | 56690..56914 | - | 225 | WP_000713561 | EexN family lipoprotein | - |
| HPG28_RS00330 | 56923..57567 | - | 645 | WP_001310442 | type IV secretion system protein | - |
| HPG28_RS00335 | 57573..58568 | - | 996 | WP_001028541 | type IV secretion system protein | virB6 |
| HPG28_RS00340 | 58572..58829 | - | 258 | WP_000739144 | hypothetical protein | - |
| HPG28_RS00345 | 58826..59179 | - | 354 | WP_023154634 | hypothetical protein | - |
| HPG28_RS00350 | 59399..59611 | - | 213 | WP_039022940 | hypothetical protein | - |
| HPG28_RS00355 | 59622..59792 | - | 171 | WP_000550720 | hypothetical protein | - |
| HPG28_RS00360 | 59796..60239 | - | 444 | WP_072037179 | NfeD family protein | - |
| HPG28_RS00365 | 60613..61566 | - | 954 | WP_072109880 | SPFH domain-containing protein | - |
| HPG28_RS00370 | 61593..61769 | - | 177 | WP_000753050 | hypothetical protein | - |
| HPG28_RS00375 | 61762..61977 | - | 216 | WP_001127357 | DUF1187 family protein | - |
| HPG28_RS00380 | 61970..62476 | - | 507 | WP_171265265 | CaiF/GrlA family transcriptional regulator | - |
Host bacterium
| ID | 14001 | GenBank | NZ_MG299138 |
| Plasmid name | pSH275-1 | Incompatibility group | IncI2 |
| Plasmid size | 63066 bp | Coordinate of oriT [Strand] | 15108..15160 [-] |
| Host baterium | Shigella sonnei strain SH275-1 |
Cargo genes
| Drug resistance gene | mcr-1.1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |