Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 121459 |
| Name | oriT_U2785|2  |
| Organism | Citrobacter freundii isolate Citrobacter freundii str. U2785 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_LS992184 (88823..88973 [-], 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_U2785|2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 13530 | GenBank | WP_001326173 |
| Name | mobH_CFU2785_RS25545_U2785|2 |
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 | 15833 | GenBank | WP_000178857 |
| Name | traD_CFU2785_RS25540_U2785|2 |
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: 81799..90889
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| CFU2785_RS26800 | 76824..77189 | - | 366 | Protein_90 | LuxR family transcriptional regulator | - |
| CFU2785_RS25460 (CFU2785_05095) | 77446..77763 | + | 318 | WP_000118520 | quaternary ammonium compound efflux SMR transporter SugE | - |
| CFU2785_RS25465 (CFU2785_05096) | 77760..78293 | - | 534 | WP_001221666 | lipocalin family protein | - |
| CFU2785_RS25470 (CFU2785_05097) | 78387..79532 | - | 1146 | WP_000976514 | extended-spectrum class C beta-lactamase CMY-2 | - |
| CFU2785_RS25475 (CFU2785_05099) | 79856..81118 | - | 1263 | WP_000608644 | IS1380-like element ISEcp1 family transposase | - |
| CFU2785_RS25480 (CFU2785_05100) | 81403..81795 | - | 393 | WP_000479535 | TraA family conjugative transfer protein | - |
| CFU2785_RS25485 (CFU2785_05101) | 81799..82377 | - | 579 | WP_000793435 | type IV conjugative transfer system lipoprotein TraV | traV |
| CFU2785_RS25490 (CFU2785_05102) | 82374..83687 | - | 1314 | WP_024131605 | TraB/VirB10 family protein | traB |
| CFU2785_RS25495 (CFU2785_05103) | 83687..84604 | - | 918 | WP_000794249 | type-F conjugative transfer system secretin TraK | traK |
| CFU2785_RS25500 (CFU2785_05104) | 84588..85214 | - | 627 | WP_001049717 | TraE/TraK family type IV conjugative transfer system protein | traE |
| CFU2785_RS25505 (CFU2785_05105) | 85211..85492 | - | 282 | WP_000805625 | type IV conjugative transfer system protein TraL | traL |
| CFU2785_RS25510 (CFU2785_05106) | 85637..86002 | - | 366 | WP_001052530 | hypothetical protein | - |
| CFU2785_RS26375 (CFU2785_05107) | 86014..86157 | - | 144 | WP_001275801 | hypothetical protein | - |
| CFU2785_RS25515 (CFU2785_05108) | 86338..87000 | - | 663 | WP_001231464 | hypothetical protein | - |
| CFU2785_RS25520 (CFU2785_05109) | 87000..87377 | - | 378 | WP_000869297 | hypothetical protein | - |
| CFU2785_RS25525 (CFU2785_05110) | 87387..87833 | - | 447 | WP_000122507 | hypothetical protein | - |
| CFU2785_RS25530 (CFU2785_05111) | 87843..88472 | - | 630 | WP_000743449 | DUF4400 domain-containing protein | tfc7 |
| CFU2785_RS25535 (CFU2785_05112) | 88429..88974 | - | 546 | WP_000228720 | hypothetical protein | - |
| CFU2785_RS25540 (CFU2785_05113) | 89024..90889 | - | 1866 | WP_000178857 | conjugative transfer system coupling protein TraD | virb4 |
| CFU2785_RS25545 (CFU2785_05114) | 90886..93858 | - | 2973 | WP_001326173 | MobH family relaxase | - |
| CFU2785_RS25550 (CFU2785_05115) | 94026..94643 | + | 618 | WP_001249395 | hypothetical protein | - |
| CFU2785_RS25555 | 94625..94858 | + | 234 | WP_001191890 | hypothetical protein | - |
Host bacterium
| ID | 21886 | GenBank | NZ_LS992184 |
| Plasmid name | U2785|2 | Incompatibility group | IncA/C2 |
| Plasmid size | 185156 bp | Coordinate of oriT [Strand] | 88823..88973 [-] |
| Host baterium | Citrobacter freundii isolate Citrobacter freundii str. U2785 |
Cargo genes
| Drug resistance gene | msr(E), mph(E), floR, tet(A), blaCMY-2, sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, blaCTX-M-15, ARR-3, cmlA1, blaOXA-10, ant(3'')-Ia, qacE, sul1, armA |
| Virulence gene | - |
| Metal resistance gene | merR, merT, merP, merA, merB, merD, merE |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |