Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113252 |
| Name | oriT_pRM094_1  |
| Organism | Salmonella enterica subsp. enterica serovar Dublin strain RM094 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP117360 (31023..31173 [-], 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_pRM094_1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8501 | GenBank | WP_001326173 |
| Name | mobH_PQP87_RS23990_pRM094_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 | 9809 | GenBank | WP_077779971 |
| Name | traD_PQP87_RS23985_pRM094_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: 23999..33089
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PQP87_RS23900 (PQP87_23900) | 19018..19197 | + | 180 | Protein_31 | helix-turn-helix domain-containing protein | - |
| PQP87_RS23905 (PQP87_23905) | 19262..19966 | + | 705 | WP_001067855 | IS6-like element IS26 family transposase | - |
| PQP87_RS23910 (PQP87_23910) | 19912..20493 | - | 582 | WP_058663077 | lipocalin family protein | - |
| PQP87_RS23915 (PQP87_23915) | 20587..21732 | - | 1146 | WP_000976514 | extended-spectrum class C beta-lactamase CMY-2 | - |
| PQP87_RS23920 (PQP87_23920) | 22056..23318 | - | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| PQP87_RS23925 (PQP87_23925) | 23603..23995 | - | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| PQP87_RS23930 (PQP87_23930) | 23999..24577 | - | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| PQP87_RS23935 (PQP87_23935) | 24574..25887 | - | 1314 | WP_024131605 | TraB/VirB10 family protein | traB |
| PQP87_RS23940 (PQP87_23940) | 25887..26804 | - | 918 | WP_000794249 | type-F conjugative transfer system secretin TraK | traK |
| PQP87_RS23945 (PQP87_23945) | 26788..27414 | - | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| PQP87_RS23950 (PQP87_23950) | 27411..27692 | - | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| PQP87_RS23955 (PQP87_23955) | 27837..28202 | - | 366 | WP_001052530 | hypothetical protein | - |
| PQP87_RS23960 (PQP87_23960) | 28538..29200 | - | 663 | WP_001231464 | hypothetical protein | - |
| PQP87_RS23965 (PQP87_23965) | 29200..29577 | - | 378 | WP_000869297 | hypothetical protein | - |
| PQP87_RS23970 (PQP87_23970) | 29587..30033 | - | 447 | WP_000122507 | hypothetical protein | - |
| PQP87_RS23975 (PQP87_23975) | 30043..30672 | - | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| PQP87_RS23980 (PQP87_23980) | 30629..31174 | - | 546 | WP_000228720 | hypothetical protein | - |
| PQP87_RS23985 (PQP87_23985) | 31224..33089 | - | 1866 | WP_077779971 | conjugative transfer system coupling protein TraD | virb4 |
| PQP87_RS23990 (PQP87_23990) | 33086..36058 | - | 2973 | WP_001326173 | MobH family relaxase | - |
| PQP87_RS23995 (PQP87_23995) | 36226..36843 | + | 618 | WP_001249395 | hypothetical protein | - |
| PQP87_RS24000 (PQP87_24000) | 36825..37058 | + | 234 | WP_001191890 | hypothetical protein | - |
Host bacterium
| ID | 13687 | GenBank | NZ_CP117360 |
| Plasmid name | pRM094_1 | Incompatibility group | IncA/C2 |
| Plasmid size | 101652 bp | Coordinate of oriT [Strand] | 31023..31173 [-] |
| Host baterium | Salmonella enterica subsp. enterica serovar Dublin strain RM094 |
Cargo genes
| Drug resistance gene | blaCMY-2, sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR, blaTEM-1B |
| Virulence gene | - |
| Metal resistance gene | merE, merD, merB, merA, merP, merT, merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |