Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 104156 |
| Name | oriT_pCB00028_3  |
| Organism | Citrobacter freundii strain CB00028 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_OP378605 (31150..31249 [-], 100 nt) |
| oriT length | 100 nt |
| IRs (inverted repeats) | 34..41, 44..51 (AGTGCGAT..ATCGCACT) 20..25, 39..44 (TAAATC..GATTTA) |
| Location of nic site | 62..63 |
| Conserved sequence flanking the nic site |
GGTGTATAGC |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 100 nt
>oriT_pCB00028_3
TATTGAATGTTTTATTCTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATCAGTTTGGTAG
TATTGAATGTTTTATTCTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATCAGTTTGGTAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3053 | GenBank | WP_020323154 |
| Name | mobF_PWC10_RS00210_pCB00028_3 |
UniProt ID | A0A0R8CGS3 |
| Length | 1072 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1072 a.a. Molecular weight: 118689.40 Da Isoelectric Point: 6.4933
>WP_020323154.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNGQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFHVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGATEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKGRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSYGHDDGQQAKSYGHEAGQQTGEKENTMKNATEAAHDGPD
TSGTENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARD
VELPQHEHENHQHDYDKEGYGL
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNGQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFHVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGATEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKGRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSYGHDDGQQAKSYGHEAGQQTGEKENTMKNATEAAHDGPD
TSGTENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARD
VELPQHEHENHQHDYDKEGYGL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A0R8CGS3 |
T4CP
| ID | 2940 | GenBank | WP_020323171 |
| Name | t4cp2_PWC10_RS00205_pCB00028_3 |
UniProt ID | _ |
| Length | 510 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 510 a.a. Molecular weight: 58208.12 Da Isoelectric Point: 9.7037
>WP_020323171.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVSIIAGSVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGRDKRVILDPNGEYVETFYRENDIILNPYDKRSPGWSMFNEIRDEFDYDLYAVSIIQ
ESKERSAEEWYRYGRLLYREVSKKLLTHKRNPSMEEVLYWCNVAEYDKVKDFVKGTPAESLFIKGAERAT
GSARFVLGDKLASHLKMPEGNFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTFSQLVERYGINIAETLLGSMRSGIVMGSSRL
GKATLEHMSRALGEIEGEIERRQGSLLQSGPNNRPRIETRTVRAVTPTEISELRNLTGYIYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVSIIAGSVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGRDKRVILDPNGEYVETFYRENDIILNPYDKRSPGWSMFNEIRDEFDYDLYAVSIIQ
ESKERSAEEWYRYGRLLYREVSKKLLTHKRNPSMEEVLYWCNVAEYDKVKDFVKGTPAESLFIKGAERAT
GSARFVLGDKLASHLKMPEGNFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTFSQLVERYGINIAETLLGSMRSGIVMGSSRL
GKATLEHMSRALGEIEGEIERRQGSLLQSGPNNRPRIETRTVRAVTPTEISELRNLTGYIYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 31820..49316
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| PWC10_RS00160 | 27146..27415 | + | 270 | WP_020323374 | hypothetical protein | - |
| PWC10_RS00165 | 27457..28284 | + | 828 | WP_202195859 | DUF5417 domain-containing protein | - |
| PWC10_RS00170 | 28466..28672 | + | 207 | WP_020323152 | DUF905 family protein | - |
| PWC10_RS00175 | 28746..28928 | + | 183 | WP_000170167 | hypothetical protein | - |
| PWC10_RS00180 | 28987..29358 | - | 372 | WP_227665545 | hypothetical protein | - |
| PWC10_RS00185 | 29401..29769 | - | 369 | WP_032416596 | plasmid stabilization protein StbC | - |
| PWC10_RS00190 | 29772..30488 | - | 717 | WP_020323147 | StbB family protein | - |
| PWC10_RS00195 | 30497..30928 | - | 432 | WP_020323173 | plasmid stabilization protein StbA | - |
| PWC10_RS00200 | 31344..31820 | + | 477 | WP_223226686 | traK protein | - |
| PWC10_RS00205 | 31820..33352 | + | 1533 | WP_020323171 | type IV secretion system DNA-binding domain-containing protein | virb4 |
| PWC10_RS00210 | 33357..36575 | + | 3219 | WP_020323154 | MobF family relaxase | - |
| PWC10_RS00215 | 36572..37237 | + | 666 | WP_020323157 | DUF6710 family protein | - |
| PWC10_RS00220 | 37230..37592 | + | 363 | WP_020323170 | hypothetical protein | - |
| PWC10_RS00225 | 38208..38519 | - | 312 | WP_032416518 | hypothetical protein | - |
| PWC10_RS00230 | 38516..38983 | - | 468 | WP_046092601 | phospholipase D family protein | - |
| PWC10_RS00235 | 39040..40041 | - | 1002 | WP_020323165 | ATPase, T2SS/T4P/T4SS family | virB11 |
| PWC10_RS00240 | 40092..41225 | - | 1134 | WP_020323153 | type IV secretion system protein VirB10 | virB10 |
| PWC10_RS00245 | 41225..42112 | - | 888 | WP_020323166 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| PWC10_RS00250 | 42123..42818 | - | 696 | WP_001208352 | type IV secretion system protein | virB8 |
| PWC10_RS00330 | 42829..42960 | - | 132 | WP_032493177 | hypothetical protein | - |
| PWC10_RS00255 | 43037..44074 | - | 1038 | WP_020323169 | type IV secretion system protein | virB6 |
| PWC10_RS00260 | 44091..44333 | - | 243 | WP_000858958 | EexN family lipoprotein | - |
| PWC10_RS00265 | 44343..45044 | - | 702 | WP_020323143 | type IV secretion system protein | virB5 |
| PWC10_RS00270 | 45060..47633 | - | 2574 | WP_020323176 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| PWC10_RS00275 | 47634..47951 | - | 318 | WP_000462629 | VirB3 family type IV secretion system protein | virB3 |
| PWC10_RS00280 | 47991..48332 | - | 342 | WP_001121032 | TrbC/VirB2 family protein | virB2 |
| PWC10_RS00285 | 48534..49316 | - | 783 | WP_032416587 | lytic transglycosylase domain-containing protein | virB1 |
| PWC10_RS00290 | 49380..49733 | + | 354 | WP_223598071 | H-NS histone family protein | - |
| PWC10_RS00295 | 49737..50087 | + | 351 | WP_032416642 | hypothetical protein | - |
| PWC10_RS00300 | 50066..50422 | + | 357 | WP_227665546 | hypothetical protein | - |
| PWC10_RS00305 | 50426..50734 | + | 309 | WP_032416643 | hypothetical protein | - |
| PWC10_RS00310 | 51019..51204 | + | 186 | WP_006118530 | ribbon-helix-helix domain-containing protein | - |
| PWC10_RS00315 | 51201..51809 | - | 609 | WP_032449362 | recombinase family protein | - |
| PWC10_RS00320 | 51975..52307 | - | 333 | WP_020323168 | hypothetical protein | - |
Host bacterium
| ID | 4595 | GenBank | NZ_OP378605 |
| Plasmid name | pCB00028_3 | Incompatibility group | IncN3 |
| Plasmid size | 52446 bp | Coordinate of oriT [Strand] | 31150..31249 [-] |
| Host baterium | Citrobacter freundii strain CB00028 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |