Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103150 |
| Name | oriT_pSh125-m2  |
| Organism | Shigella sonnei strain SH11Sh125 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_KY363998 (13631..13683 [-], 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_pSh125-m2
CACACGATTGTAACATGACCGGAACGGTCTTGTGTACAATCGGTATCGTGCCT
CACACGATTGTAACATGACCGGAACGGTCTTGTGTACAATCGGTATCGTGCCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 2094 | GenBank | WP_015059539 |
| Name | t4cp2_HPF88_RS00240_pSh125-m2 |
UniProt ID | _ |
| Length | 652 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 652 a.a. Molecular weight: 73404.02 Da Isoelectric Point: 9.4339
>WP_015059539.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MNAKKMGGLILFLLLLLVGVLIASNYLGGYTALRYSSVDMSLLKWDTFHSVISTFSGNPQYKKLVFMAWF
GFSVPLIFFAIFMLIVVIGIMPKKVIYGDARLATDMDLSKSGFFPDKKSPYKHPPILIGKMFKGRYKKQF
IYFAGQQFLILYAPTRSGKGVGIVIPNCVNYPGSMVILDIKLENWFLSAGFRQKELGQKCFLFAPAGYAE
TIDQAIKGQIRSHRWNPLDCVSRSDLLRETDLAKIAAILIPASDDPIWSDSARNLFVGLGLYLLDKERFH
LDQKAKGHNAPDVLVSISAILKTSIPDNGKDLAAWMGQEVENRSWISDKTKSFFFEFMSAPDRTRGSIKT
NFSSPLNIFSNPVTAEATNFSDFDIRDIRKKPMSIYLGLTPDALITHEKIVNLFFSLLVNENCRELPEHN
PDLKYQCLILLDEFTSMGKSEVIERAVGFTAGYNLRFMFILQNEGQGQKSDMYGQEGWTTFTENSAVVLY
YPPKSKNALAKKISEEIGVRDMKISKRSISSGGGKGGSSRTRNDDVIERPVLLPEEIVSLRDKKNKARNI
AIREIITSEFSRPFIANKIIWFEEPEFKRRVDIARNNHVDIPNLFTQEVMDEIAKIAEIYLPKAGGKKVM
VAGGNVITNPDLDNHDKTDVSE
MNAKKMGGLILFLLLLLVGVLIASNYLGGYTALRYSSVDMSLLKWDTFHSVISTFSGNPQYKKLVFMAWF
GFSVPLIFFAIFMLIVVIGIMPKKVIYGDARLATDMDLSKSGFFPDKKSPYKHPPILIGKMFKGRYKKQF
IYFAGQQFLILYAPTRSGKGVGIVIPNCVNYPGSMVILDIKLENWFLSAGFRQKELGQKCFLFAPAGYAE
TIDQAIKGQIRSHRWNPLDCVSRSDLLRETDLAKIAAILIPASDDPIWSDSARNLFVGLGLYLLDKERFH
LDQKAKGHNAPDVLVSISAILKTSIPDNGKDLAAWMGQEVENRSWISDKTKSFFFEFMSAPDRTRGSIKT
NFSSPLNIFSNPVTAEATNFSDFDIRDIRKKPMSIYLGLTPDALITHEKIVNLFFSLLVNENCRELPEHN
PDLKYQCLILLDEFTSMGKSEVIERAVGFTAGYNLRFMFILQNEGQGQKSDMYGQEGWTTFTENSAVVLY
YPPKSKNALAKKISEEIGVRDMKISKRSISSGGGKGGSSRTRNDDVIERPVLLPEEIVSLRDKKNKARNI
AIREIITSEFSRPFIANKIIWFEEPEFKRRVDIARNNHVDIPNLFTQEVMDEIAKIAEIYLPKAGGKKVM
VAGGNVITNPDLDNHDKTDVSE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 32545..56002
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HPF88_RS00170 | 28034..29158 | - | 1125 | WP_000486716 | site-specific integrase | - |
| HPF88_RS00175 | 29296..29451 | + | 156 | WP_001358489 | hypothetical protein | - |
| HPF88_RS00180 | 29994..30323 | - | 330 | WP_097331912 | pilus assembly protein | - |
| HPF88_RS00420 | 30299..30520 | + | 222 | Protein_39 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HPF88_RS00190 | 30517..31893 | - | 1377 | WP_000750519 | shufflon system plasmid conjugative transfer pilus tip adhesin PilV | - |
| HPF88_RS00195 | 31906..32541 | - | 636 | WP_000934977 | A24 family peptidase | - |
| HPF88_RS00200 | 32545..33027 | - | 483 | WP_001258095 | lytic transglycosylase domain-containing protein | virB1 |
| HPF88_RS00205 | 33093..33650 | - | 558 | WP_000095048 | type 4 pilus major pilin | - |
| HPF88_RS00210 | 33695..34804 | - | 1110 | WP_000974903 | type II secretion system F family protein | - |
| HPF88_RS00215 | 34795..36333 | - | 1539 | WP_000466225 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HPF88_RS00220 | 36358..36852 | - | 495 | WP_171264651 | type IV pilus biogenesis protein PilP | - |
| HPF88_RS00225 | 36836..38158 | - | 1323 | WP_000454142 | type 4b pilus protein PilO2 | - |
| HPF88_RS00230 | 38197..39840 | - | 1644 | WP_001035592 | PilN family type IVB pilus formation outer membrane protein | - |
| HPF88_RS00235 | 39833..40369 | - | 537 | WP_001220543 | sigma 54-interacting transcriptional regulator | virb4 |
| HPF88_RS00240 | 40416..42374 | - | 1959 | WP_015059539 | type IV secretory system conjugative DNA transfer family protein | - |
| HPF88_RS00245 | 42390..43445 | - | 1056 | WP_001059977 | P-type DNA transfer ATPase VirB11 | virB11 |
| HPF88_RS00250 | 43464..44603 | - | 1140 | WP_171264649 | TrbI/VirB10 family protein | virB10 |
| HPF88_RS00255 | 44593..45294 | - | 702 | WP_000274524 | TrbG/VirB9 family P-type conjugative transfer protein | - |
| HPF88_RS00260 | 45360..46094 | - | 735 | WP_000432282 | type IV secretion system protein | virB8 |
| HPF88_RS00265 | 46260..48617 | - | 2358 | WP_063078682 | VirB4 family type IV secretion system protein | virb4 |
| HPF88_RS00270 | 48623..48943 | - | 321 | WP_000362080 | VirB3 family type IV secretion system protein | virB3 |
| HPF88_RS00405 | 49014..49304 | - | 291 | WP_000865479 | conjugal transfer protein | - |
| HPF88_RS00280 | 49304..49888 | - | 585 | WP_001177113 | lytic transglycosylase domain-containing protein | virB1 |
| HPF88_RS00285 | 49909..50307 | - | 399 | WP_001153665 | hypothetical protein | - |
| HPF88_RS00290 | 50426..50863 | - | 438 | WP_000539665 | type IV pilus biogenesis protein PilM | - |
| HPF88_RS00295 | 50869..52104 | - | 1236 | WP_015059538 | TcpQ domain-containing protein | - |
| HPF88_RS00300 | 52107..52406 | - | 300 | WP_000835764 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| HPF88_RS00305 | 52474..52755 | - | 282 | WP_000638823 | type II toxin-antitoxin system RelE/ParE family toxin | - |
| HPF88_RS00310 | 52745..52996 | - | 252 | WP_000121741 | hypothetical protein | - |
| HPF88_RS00315 | 53096..53731 | - | 636 | WP_015059536 | hypothetical protein | - |
| HPF88_RS00320 | 53804..54091 | - | 288 | WP_001032611 | EexN family lipoprotein | - |
| HPF88_RS00325 | 54104..54358 | - | 255 | WP_001043555 | EexN family lipoprotein | - |
| HPF88_RS00330 | 54360..55001 | - | 642 | WP_001425343 | type IV secretion system protein | - |
| HPF88_RS00335 | 55007..56002 | - | 996 | WP_001028543 | type IV secretion system protein | virB6 |
| HPF88_RS00340 | 56006..56263 | - | 258 | WP_000739144 | hypothetical protein | - |
| HPF88_RS00345 | 56260..56613 | - | 354 | WP_223286767 | hypothetical protein | - |
| HPF88_RS00350 | 56833..57279 | - | 447 | WP_001243165 | hypothetical protein | - |
| HPF88_RS00355 | 57290..57460 | - | 171 | WP_000550720 | hypothetical protein | - |
| HPF88_RS00360 | 57464..57907 | - | 444 | WP_000964330 | NfeD family protein | - |
| HPF88_RS00365 | 58281..59234 | - | 954 | WP_072089442 | SPFH domain-containing protein | - |
| HPF88_RS00370 | 59261..59437 | - | 177 | WP_000753050 | hypothetical protein | - |
| HPF88_RS00375 | 59430..59645 | - | 216 | WP_001127357 | DUF1187 family protein | - |
| HPF88_RS00380 | 59638..60144 | - | 507 | WP_001326595 | CaiF/GrlA family transcriptional regulator | - |
Host bacterium
| ID | 3593 | GenBank | NZ_KY363998 |
| Plasmid name | pSh125-m2 | Incompatibility group | IncI2 |
| Plasmid size | 60734 bp | Coordinate of oriT [Strand] | 13631..13683 [-] |
| Host baterium | Shigella sonnei strain SH11Sh125 |
Cargo genes
| Drug resistance gene | mcr-1.1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |