Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113230 |
| Name | oriT_pRM043_1  |
| Organism | Salmonella enterica subsp. enterica serovar Dublin strain RM043 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP117374 (65925..66075 [-], 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_pRM043_1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8489 | GenBank | WP_001326173 |
| Name | mobH_PQQ08_RS24245_pRM043_1 |
UniProt ID | F5BPR1 |
| Length | 990 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 990 a.a. Molecular weight: 109356.90 Da Isoelectric Point: 4.9395
>WP_001326173.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | F5BPR1 |
T4CP
| ID | 9794 | GenBank | WP_077779971 |
| Name | traD_PQQ08_RS24240_pRM043_1 |
UniProt ID | _ |
| Length | 621 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 621 a.a. Molecular weight: 69253.76 Da Isoelectric Point: 6.9403
>WP_077779971.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPVFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPVFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 58901..67991
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PQQ08_RS25055 | 53926..54291 | - | 366 | Protein_70 | LuxR family transcriptional regulator | - |
| PQQ08_RS24160 (PQQ08_24160) | 54548..54865 | + | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| PQQ08_RS24165 (PQQ08_24165) | 54862..55395 | - | 534 | WP_001221666 | lipocalin family protein | - |
| PQQ08_RS24170 (PQQ08_24170) | 55489..56634 | - | 1146 | WP_274896668 | CMY-2 family class C beta-lactamase | - |
| PQQ08_RS24175 (PQQ08_24175) | 56958..58220 | - | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| PQQ08_RS24180 (PQQ08_24180) | 58505..58897 | - | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| PQQ08_RS24185 (PQQ08_24185) | 58901..59479 | - | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| PQQ08_RS24190 (PQQ08_24190) | 59476..60789 | - | 1314 | WP_024131605 | TraB/VirB10 family protein | traB |
| PQQ08_RS24195 (PQQ08_24195) | 60789..61706 | - | 918 | WP_000794249 | type-F conjugative transfer system secretin TraK | traK |
| PQQ08_RS24200 (PQQ08_24200) | 61690..62316 | - | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| PQQ08_RS24205 (PQQ08_24205) | 62313..62594 | - | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| PQQ08_RS24210 (PQQ08_24210) | 62739..63104 | - | 366 | WP_001052530 | hypothetical protein | - |
| PQQ08_RS24215 (PQQ08_24215) | 63440..64102 | - | 663 | WP_001231464 | hypothetical protein | - |
| PQQ08_RS24220 (PQQ08_24220) | 64102..64479 | - | 378 | WP_000869297 | hypothetical protein | - |
| PQQ08_RS24225 (PQQ08_24225) | 64489..64935 | - | 447 | WP_000122507 | hypothetical protein | - |
| PQQ08_RS24230 (PQQ08_24230) | 64945..65574 | - | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| PQQ08_RS24235 (PQQ08_24235) | 65531..66076 | - | 546 | WP_000228720 | hypothetical protein | - |
| PQQ08_RS24240 (PQQ08_24240) | 66126..67991 | - | 1866 | WP_077779971 | conjugative transfer system coupling protein TraD | virb4 |
| PQQ08_RS24245 (PQQ08_24245) | 67988..70960 | - | 2973 | WP_001326173 | MobH family relaxase | - |
| PQQ08_RS24250 (PQQ08_24250) | 71128..71745 | + | 618 | WP_001249395 | hypothetical protein | - |
| PQQ08_RS24255 (PQQ08_24255) | 71727..71960 | + | 234 | WP_001191890 | hypothetical protein | - |
Host bacterium
| ID | 13665 | GenBank | NZ_CP117374 |
| Plasmid name | pRM043_1 | Incompatibility group | IncA/C2 |
| Plasmid size | 106220 bp | Coordinate of oriT [Strand] | 65925..66075 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Dublin strain RM043 |
Cargo genes
| Drug resistance gene | blaTEM-1B, blaCMY-2, sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR |
| Virulence gene | - |
| Metal resistance gene | merR, merT, merP, merA, merB, merD, merE |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |