Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 121597 |
| Name | oriT_pD18-1  |
| Organism | Citrobacter freundii strain 18-1 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP022277 (19602..19691 [+], 90 nt) |
| oriT length | 90 nt |
| IRs (inverted repeats) | 34..41, 44..51 (AGTGCGAT..ATCGCACT) |
| Location of nic site | 62..63 |
| Conserved sequence flanking the nic site |
GGTGTATAGC |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 90 nt
>oriT_pD18-1
TATTTCATTTTTTGTTTTTTTAATCAGTTAGTTAGTGCGATTCATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC
TATTTCATTTTTTGTTTTTTTAATCAGTTAGTTAGTGCGATTCATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 13620 | GenBank | WP_024561907 |
| Name | mobF_CFA70_RS28765_pD18-1 |
UniProt ID | H1ZMV6 |
| Length | 1072 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1072 a.a. Molecular weight: 118896.59 Da Isoelectric Point: 6.4636
>WP_024561907.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSYGHSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPD
TSGTENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARD
VELPQHEHENHQHDHDKEGYGL
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSYGHSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPD
TSGTENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARD
VELPQHEHENHQHDHDKEGYGL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | H1ZMV6 |
T4CP
| ID | 15920 | GenBank | WP_032493179 |
| Name | t4cp2_CFA70_RS28770_pD18-1 |
UniProt ID | _ |
| Length | 510 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 510 a.a. Molecular weight: 57912.96 Da Isoelectric Point: 9.5127
>WP_032493179.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERDHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGTDKRIVLDPNGEYVETFYRPGDVILSPYDKRSPGWSMFNEIRDDFDYDLYAVSIIQ
ESKERSAEEWYRYGRLIYREVSKKLLTLKRSPTMEEVMHWCTIVENEKLKEFVKGTPAEALFIKGAERAT
GSARFVLGDKLAPHLKMPAGDFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTYSQLIERYGINIAETLLGSMRSGIVMGSSRL
GKETLEQMSRALGEIEGEVEHKQGNPFQAGIGNRPRIETRTVRAVTPTEISELKNLTGYVYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERDHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGTDKRIVLDPNGEYVETFYRPGDVILSPYDKRSPGWSMFNEIRDDFDYDLYAVSIIQ
ESKERSAEEWYRYGRLIYREVSKKLLTLKRSPTMEEVMHWCTIVENEKLKEFVKGTPAEALFIKGAERAT
GSARFVLGDKLAPHLKMPAGDFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTYSQLIERYGINIAETLLGSMRSGIVMGSSRL
GKETLEQMSRALGEIEGEVEHKQGNPFQAGIGNRPRIETRTVRAVTPTEISELKNLTGYVYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 744..19032
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| CFA70_RS29925 (CFA70_28685) | 744..1091 | + | 348 | WP_088903451 | hypothetical protein | virb4 |
| CFA70_RS29930 | 1022..1426 | + | 405 | WP_232481339 | hypothetical protein | virb4 |
| CFA70_RS29935 | 1790..2137 | + | 348 | WP_232481340 | hypothetical protein | virb4 |
| CFA70_RS28690 (CFA70_28695) | 2323..2841 | + | 519 | WP_232481350 | type IV secretion system protein | virB5 |
| CFA70_RS28695 (CFA70_28700) | 2851..3093 | + | 243 | WP_000858958 | EexN family lipoprotein | - |
| CFA70_RS29940 | 3110..3391 | + | 282 | WP_232481342 | hypothetical protein | virB6 |
| CFA70_RS28700 (CFA70_28705) | 3382..4146 | + | 765 | WP_232481343 | type IV secretion system protein | virB6 |
| CFA70_RS30080 (CFA70_28710) | 4223..4354 | + | 132 | WP_032493177 | hypothetical protein | - |
| CFA70_RS28710 (CFA70_28715) | 4365..5060 | + | 696 | WP_001208352 | type IV secretion system protein | virB8 |
| CFA70_RS28715 (CFA70_28720) | 5203..5955 | + | 753 | WP_232481344 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| CFA70_RS28720 (CFA70_28725) | 5955..7088 | + | 1134 | WP_000101920 | type IV secretion system protein VirB10 | virB10 |
| CFA70_RS28725 (CFA70_28730) | 7045..7371 | + | 327 | WP_232481345 | hypothetical protein | - |
| CFA70_RS28730 (CFA70_28735) | 7368..7973 | - | 606 | WP_000509966 | recombinase family protein | - |
| CFA70_RS28735 (CFA70_28740) | 8068..10965 | + | 2898 | WP_023307208 | Tn3-like element Tn5403 family transposase | - |
| CFA70_RS28740 (CFA70_28745) | 11017..11808 | + | 792 | WP_232481348 | ATPase, T2SS/T4P/T4SS family | virB11 |
| CFA70_RS28745 (CFA70_28750) | 11820..12332 | + | 513 | WP_029697418 | phospholipase D family protein | - |
| CFA70_RS28750 (CFA70_28755) | 12329..12640 | + | 312 | WP_000570332 | hypothetical protein | - |
| CFA70_RS28755 (CFA70_28760) | 13260..13622 | - | 363 | WP_024561906 | hypothetical protein | - |
| CFA70_RS28760 (CFA70_28765) | 13615..14280 | - | 666 | WP_000971716 | DUF6710 family protein | - |
| CFA70_RS28765 (CFA70_28770) | 14277..17495 | - | 3219 | WP_024561907 | MobF family relaxase | - |
| CFA70_RS28770 (CFA70_28775) | 17500..19032 | - | 1533 | WP_032493179 | type IV secretion system DNA-binding domain-containing protein | virb4 |
| CFA70_RS29945 | 19032..19508 | - | 477 | WP_001238978 | hypothetical protein | - |
| CFA70_RS28780 (CFA70_28785) | 19923..20354 | + | 432 | WP_029697170 | plasmid stabilization protein StbA | - |
| CFA70_RS28785 (CFA70_28790) | 20363..21079 | + | 717 | WP_032493181 | StbB family protein | - |
| CFA70_RS28790 (CFA70_28795) | 21082..21450 | + | 369 | WP_000360828 | plasmid stabilization protein StbC | - |
| CFA70_RS29950 | 21512..21862 | + | 351 | WP_014014961 | hypothetical protein | - |
| CFA70_RS28800 (CFA70_28805) | 21921..22103 | - | 183 | WP_032493182 | hypothetical protein | - |
| CFA70_RS28805 (CFA70_28810) | 22178..22384 | - | 207 | WP_032493183 | DUF905 family protein | - |
| CFA70_RS29200 | 22534..22791 | + | 258 | WP_157676234 | hypothetical protein | - |
| CFA70_RS28810 (CFA70_28815) | 23164..23661 | - | 498 | WP_032493186 | MucR family transcriptional regulator | - |
| CFA70_RS28815 (CFA70_28820) | 23716..23916 | - | 201 | WP_015060066 | hypothetical protein | - |
Host bacterium
| ID | 22024 | GenBank | NZ_CP022277 |
| Plasmid name | pD18-1 | Incompatibility group | IncN3 |
| Plasmid size | 43109 bp | Coordinate of oriT [Strand] | 19602..19691 [+] |
| Host baterium | Citrobacter freundii strain 18-1 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |