Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113238 |
| Name | oriT_pRM037_1  |
| Organism | Salmonella enterica subsp. enterica serovar Newport strain RM037 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP117381 (50155..50305 [+], 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_pRM037_1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8494 | GenBank | WP_001326173 |
| Name | mobH_PQP93_RS24015_pRM037_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 | 9801 | GenBank | WP_000178857 |
| Name | traD_PQP93_RS24020_pRM037_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: 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: 48239..57329
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PQP93_RS24005 (PQP93_24005) | 44270..44503 | - | 234 | WP_001191890 | hypothetical protein | - |
| PQP93_RS24010 (PQP93_24010) | 44485..45102 | - | 618 | WP_001249395 | hypothetical protein | - |
| PQP93_RS24015 (PQP93_24015) | 45270..48242 | + | 2973 | WP_001326173 | MobH family relaxase | - |
| PQP93_RS24020 (PQP93_24020) | 48239..50104 | + | 1866 | WP_000178857 | conjugative transfer system coupling protein TraD | virb4 |
| PQP93_RS24025 (PQP93_24025) | 50154..50699 | + | 546 | WP_000228720 | hypothetical protein | - |
| PQP93_RS24030 (PQP93_24030) | 50656..51285 | + | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| PQP93_RS24035 (PQP93_24035) | 51295..51741 | + | 447 | WP_000122507 | hypothetical protein | - |
| PQP93_RS24040 (PQP93_24040) | 51751..52128 | + | 378 | WP_000869297 | hypothetical protein | - |
| PQP93_RS24045 (PQP93_24045) | 52128..52790 | + | 663 | WP_001231464 | hypothetical protein | - |
| PQP93_RS24050 (PQP93_24050) | 53126..53491 | + | 366 | WP_001052530 | hypothetical protein | - |
| PQP93_RS24055 (PQP93_24055) | 53636..53917 | + | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| PQP93_RS24060 (PQP93_24060) | 53914..54540 | + | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| PQP93_RS24065 (PQP93_24065) | 54524..55441 | + | 918 | WP_274890347 | type-F conjugative transfer system secretin TraK | traK |
| PQP93_RS24070 (PQP93_24070) | 55441..56754 | + | 1314 | WP_274890352 | TraB/VirB10 family protein | traB |
| PQP93_RS24075 (PQP93_24075) | 56751..57329 | + | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| PQP93_RS24080 (PQP93_24080) | 57333..57725 | + | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| PQP93_RS24085 (PQP93_24085) | 58010..59272 | + | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| PQP93_RS24090 (PQP93_24090) | 59596..60741 | + | 1146 | WP_000976514 | extended-spectrum class C beta-lactamase CMY-2 | - |
| PQP93_RS24095 (PQP93_24095) | 60835..61368 | + | 534 | WP_001221666 | lipocalin family protein | - |
| PQP93_RS24100 (PQP93_24100) | 61365..61682 | - | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| PQP93_RS24405 | 61939..62304 | + | 366 | Protein_86 | LuxR family transcriptional regulator | - |
Host bacterium
| ID | 13673 | GenBank | NZ_CP117381 |
| Plasmid name | pRM037_1 | Incompatibility group | IncA/C2 |
| Plasmid size | 99202 bp | Coordinate of oriT [Strand] | 50155..50305 [+] |
| Host baterium | Salmonella enterica subsp. enterica serovar Newport strain RM037 |
Cargo genes
| Drug resistance gene | floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCMY-2 |
| Virulence gene | - |
| Metal resistance gene | merE, merD, merB, merA, merP, merT, merR |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |