Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114080 |
| Name | oriT_pR18.0872_16k  |
| Organism | Salmonella enterica subsp. enterica serovar Thompson strain R18.0872 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP100706 (13197..13347 [+], 151 nt) |
| oriT length | 151 nt |
| IRs (inverted repeats) | 93..98, 106..111 (TGGCCT..AGGCCA) 12..17, 24..29 (AACCCT..AGGGTT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 151 nt
>oriT_pR18.0872_16k
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 10471 | GenBank | WP_000178857 |
| Name | traD_NL734_RS24925_pR18.0872_16k |
UniProt ID | _ |
| Length | 621 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 621 a.a. Molecular weight: 69225.71 Da Isoelectric Point: 6.9403
>WP_000178857.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 818..14327
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| NL734_RS24860 (NL734_24860) | 308..673 | + | 366 | WP_001052530 | hypothetical protein | - |
| NL734_RS24865 (NL734_24865) | 818..1099 | + | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| NL734_RS24870 (NL734_24870) | 1096..1722 | + | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| NL734_RS24875 (NL734_24875) | 1706..2623 | + | 918 | WP_000794249 | type-F conjugative transfer system secretin TraK | traK |
| NL734_RS24880 (NL734_24880) | 2623..3936 | + | 1314 | WP_024131605 | TraB/VirB10 family protein | traB |
| NL734_RS24885 (NL734_24885) | 3933..4511 | + | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| NL734_RS24890 (NL734_24890) | 4515..4907 | + | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| NL734_RS24895 (NL734_24895) | 5192..6454 | + | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| NL734_RS24900 (NL734_24900) | 6778..7923 | + | 1146 | WP_000976514 | extended-spectrum class C beta-lactamase CMY-2 | - |
| NL734_RS24905 (NL734_24905) | 8017..8550 | + | 534 | WP_001221666 | lipocalin family protein | - |
| NL734_RS24910 (NL734_24910) | 8547..8864 | - | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| NL734_RS24915 (NL734_24915) | 9121..9312 | + | 192 | Protein_11 | hypothetical protein | - |
| NL734_RS24920 (NL734_24920) | 9473..11284 | + | 1812 | WP_254521175 | hypothetical protein | - |
| NL734_RS24925 (NL734_24925) | 11281..13146 | + | 1866 | WP_000178857 | conjugative transfer system coupling protein TraD | virb4 |
| NL734_RS24930 (NL734_24930) | 13196..13741 | + | 546 | WP_000228720 | hypothetical protein | - |
| NL734_RS24935 (NL734_24935) | 13698..14327 | + | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| NL734_RS24940 (NL734_24940) | 14337..14783 | + | 447 | WP_000122507 | hypothetical protein | - |
| NL734_RS24945 (NL734_24945) | 14793..15170 | + | 378 | WP_000869297 | hypothetical protein | - |
| NL734_RS24950 (NL734_24950) | 15170..15832 | + | 663 | WP_001231464 | hypothetical protein | - |
Host bacterium
| ID | 14515 | GenBank | NZ_CP100706 |
| Plasmid name | pR18.0872_16k | Incompatibility group | - |
| Plasmid size | 15860 bp | Coordinate of oriT [Strand] | 13197..13347 [+] |
| Host baterium | Salmonella enterica subsp. enterica serovar Thompson strain R18.0872 |
Cargo genes
| Drug resistance gene | blaCMY-2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |