Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 114633 |
| Name | oriT_Y3|unnamed1  |
| Organism | Citrobacter sp. Y3 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP050010 (31914..31996 [+], 83 nt) |
| oriT length | 83 nt |
| IRs (inverted repeats) | 27..34, 37..44 (AGTGCGAT..ATCGCACT) 13..18, 32..37 (TAAATC..GATTTA) |
| Location of nic site | 55..56 |
| Conserved sequence flanking the nic site |
GGTGTATAGC |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 83 nt
>oriT_Y3|unnamed1
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 9385 | GenBank | WP_024561907 |
| Name | mobF_HAP28_RS25530_Y3|unnamed1 |
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 | 10894 | GenBank | WP_000139145 |
| Name | t4cp2_HAP28_RS25535_Y3|unnamed1 |
UniProt ID | _ |
| Length | 510 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 510 a.a. Molecular weight: 57854.92 Da Isoelectric Point: 9.5852
>WP_000139145.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGTDKRIVLDPNGEYVETFYRPGDVILSPYDKRSPGWSMFNEIRDDFDYDLYAVSIIQ
ESKERSAEEWYRYGRLIYREVSKKLLTLKRSPTMEEVMHWCTIVENEKLKEFVKGTPAEALFIKGAERAT
GSARFVLGDKLAPHLKMPAGDFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTYSQLIERYGINIAETLLGSMRSGIVMGSSRL
GKETLEQMSRALGEIEGEVEHKQGNPFQAGIGNRPRIETRTVRAVTPTEISELKNLTGYVYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
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: 13827..31336
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HAP28_RS25410 (HAP28_25410) | 9505..10386 | - | 882 | WP_024562123 | replication protein RepA | - |
| HAP28_RS25415 (HAP28_25415) | 10537..10731 | + | 195 | WP_071790232 | hypothetical protein | - |
| HAP28_RS25420 (HAP28_25420) | 10964..11209 | + | 246 | WP_166444322 | hypothetical protein | - |
| HAP28_RS25425 (HAP28_25425) | 11334..11942 | + | 609 | WP_071646442 | recombinase family protein | - |
| HAP28_RS25430 (HAP28_25430) | 11939..12124 | - | 186 | WP_024562121 | ribbon-helix-helix domain-containing protein | - |
| HAP28_RS25435 (HAP28_25435) | 12409..12717 | - | 309 | WP_166444323 | hypothetical protein | - |
| HAP28_RS25440 (HAP28_25440) | 12721..13059 | - | 339 | WP_000040982 | hypothetical protein | - |
| HAP28_RS25445 (HAP28_25445) | 13056..13406 | - | 351 | WP_079896996 | hypothetical protein | - |
| HAP28_RS25450 (HAP28_25450) | 13410..13727 | - | 318 | WP_032449361 | H-NS histone family protein | - |
| HAP28_RS25455 (HAP28_25455) | 13827..14609 | + | 783 | WP_166444324 | lytic transglycosylase domain-containing protein | virB1 |
| HAP28_RS25460 (HAP28_25460) | 14856..15152 | + | 297 | WP_015060075 | TrbC/VirB2 family protein | virB2 |
| HAP28_RS25465 (HAP28_25465) | 15192..15509 | + | 318 | WP_000462629 | type IV secretion system protein VirB3 | virB3 |
| HAP28_RS25470 (HAP28_25470) | 15510..18083 | + | 2574 | WP_166444325 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| HAP28_RS25475 (HAP28_25475) | 18099..18809 | + | 711 | WP_024562118 | type IV secretion system protein | virB5 |
| HAP28_RS25480 (HAP28_25480) | 18819..19061 | + | 243 | WP_000858958 | EexN family lipoprotein | - |
| HAP28_RS25485 (HAP28_25485) | 19078..20115 | + | 1038 | WP_079917022 | type IV secretion system protein | virB6 |
| HAP28_RS25490 (HAP28_25490) | 20334..21029 | + | 696 | WP_001208352 | type IV secretion system protein | virB8 |
| HAP28_RS25495 (HAP28_25495) | 21040..21927 | + | 888 | WP_000758230 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| HAP28_RS25500 (HAP28_25500) | 21927..23060 | + | 1134 | WP_000101920 | type IV secretion system protein VirB10 | virB10 |
| HAP28_RS25505 (HAP28_25505) | 23111..24112 | + | 1002 | WP_166444326 | ATPase, T2SS/T4P/T4SS family | virB11 |
| HAP28_RS25510 (HAP28_25510) | 24124..24636 | + | 513 | WP_029697418 | phospholipase D family protein | - |
| HAP28_RS25515 (HAP28_25515) | 24633..24944 | + | 312 | WP_000570332 | hypothetical protein | - |
| HAP28_RS25520 (HAP28_25520) | 25564..25926 | - | 363 | WP_024561906 | hypothetical protein | - |
| HAP28_RS25525 (HAP28_25525) | 25919..26584 | - | 666 | WP_166444327 | DUF6710 family protein | - |
| HAP28_RS25530 (HAP28_25530) | 26581..29799 | - | 3219 | WP_024561907 | MobF family relaxase | - |
| HAP28_RS25535 (HAP28_25535) | 29804..31336 | - | 1533 | WP_000139145 | type IV secretion system DNA-binding domain-containing protein | virb4 |
| HAP28_RS26405 (HAP28_25540) | 31336..31812 | - | 477 | WP_001238978 | hypothetical protein | - |
| HAP28_RS25545 | 32228..32659 | + | 432 | WP_166444328 | plasmid stabilization protein StbA | - |
| HAP28_RS25550 (HAP28_25550) | 32668..33384 | + | 717 | WP_000861579 | StbB family protein | - |
| HAP28_RS25555 (HAP28_25555) | 33387..33755 | + | 369 | WP_166444329 | plasmid stabilization protein StbC | - |
| HAP28_RS26410 | 33817..34167 | + | 351 | WP_240935397 | hypothetical protein | - |
Host bacterium
| ID | 15068 | GenBank | NZ_CP050010 |
| Plasmid name | Y3|unnamed1 | Incompatibility group | IncN2 |
| Plasmid size | 34341 bp | Coordinate of oriT [Strand] | 31914..31996 [+] |
| Host baterium | Citrobacter sp. Y3 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |