Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113204 |
| Name | oriT_pRM008_1  |
| Organism | Salmonella enterica subsp. enterica serovar Uganda strain RM008 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP117391 (50152..50302 [+], 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_pRM008_1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 8471 | GenBank | WP_001326173 |
| Name | mobH_PQP88_RS23445_pRM008_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 | 9773 | GenBank | WP_274890608 |
| Name | traD_PQP88_RS23450_pRM008_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: 69209.71 Da Isoelectric Point: 6.9403
>WP_274890608.1 conjugative transfer system coupling protein TraD [Salmonella enterica]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGREATVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGREATVKKVVRKI
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: 48236..57326
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PQP88_RS23435 (PQP88_23435) | 44267..44500 | - | 234 | WP_001191890 | hypothetical protein | - |
| PQP88_RS23440 (PQP88_23440) | 44482..45099 | - | 618 | WP_001249395 | hypothetical protein | - |
| PQP88_RS23445 (PQP88_23445) | 45267..48239 | + | 2973 | WP_001326173 | MobH family relaxase | - |
| PQP88_RS23450 (PQP88_23450) | 48236..50101 | + | 1866 | WP_274890608 | conjugative transfer system coupling protein TraD | virb4 |
| PQP88_RS23455 (PQP88_23455) | 50151..50696 | + | 546 | WP_000228720 | hypothetical protein | - |
| PQP88_RS23460 (PQP88_23460) | 50653..51282 | + | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| PQP88_RS23465 (PQP88_23465) | 51292..51738 | + | 447 | WP_000122507 | hypothetical protein | - |
| PQP88_RS23470 (PQP88_23470) | 51748..52125 | + | 378 | WP_000869297 | hypothetical protein | - |
| PQP88_RS23475 (PQP88_23475) | 52125..52787 | + | 663 | WP_001231464 | hypothetical protein | - |
| PQP88_RS23480 (PQP88_23480) | 53123..53488 | + | 366 | WP_001052530 | hypothetical protein | - |
| PQP88_RS23485 (PQP88_23485) | 53633..53914 | + | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| PQP88_RS23490 (PQP88_23490) | 53911..54537 | + | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| PQP88_RS23495 (PQP88_23495) | 54521..55438 | + | 918 | WP_000794249 | type-F conjugative transfer system secretin TraK | traK |
| PQP88_RS23500 (PQP88_23500) | 55438..56751 | + | 1314 | WP_024131605 | TraB/VirB10 family protein | traB |
| PQP88_RS23505 (PQP88_23505) | 56748..57326 | + | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| PQP88_RS23510 (PQP88_23510) | 57330..57722 | + | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| PQP88_RS23515 (PQP88_23515) | 58007..59269 | + | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| PQP88_RS23520 (PQP88_23520) | 59593..60738 | + | 1146 | WP_000976514 | extended-spectrum class C beta-lactamase CMY-2 | - |
| PQP88_RS23525 (PQP88_23525) | 60832..61365 | + | 534 | WP_001221666 | lipocalin family protein | - |
| PQP88_RS23530 (PQP88_23530) | 61362..61679 | - | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| PQP88_RS23840 | 61936..62301 | + | 366 | Protein_86 | LuxR family transcriptional regulator | - |
Host bacterium
| ID | 13639 | GenBank | NZ_CP117391 |
| Plasmid name | pRM008_1 | Incompatibility group | IncA/C2 |
| Plasmid size | 100521 bp | Coordinate of oriT [Strand] | 50152..50302 [+] |
| Host baterium | Salmonella enterica subsp. enterica serovar Uganda strain RM008 |
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 | - |