Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 111367 |
| Name | oriT_Yol001|pAt  |
| Organism | Agrobacterium tumefaciens strain Yol001 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP048479 (106514..106542 [+], 29 nt) |
| oriT length | 29 nt |
| IRs (inverted repeats) | 14..19, 24..29 (CGTCGC..GCGACG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 29 nt
>oriT_Yol001|pAt
AGGGCGCAATATACGTCGCTGTCGCGACG
AGGGCGCAATATACGTCGCTGTCGCGACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 7414 | GenBank | WP_099086577 |
| Name | traA_FY154_RS23955_Yol001|pAt |
UniProt ID | _ |
| Length | 1542 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1542 a.a. Molecular weight: 170138.27 Da Isoelectric Point: 7.7149
>WP_099086577.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAAELVHEELALPDQIPAWFKNAVSG
KSVAGASEVLWNAVDAFETRADAQLARELIIALPEELTRAENIAVVREFVQDNFTSKGMVADWVYHDKDG
NPHIHLMMTLRPLTEEGFGPKKVAVLGEDGEPLRVVTPHRPNGKIVYKLWAGDKETMKVWKIAWADAANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGVEMYFAPADLARRQDMADRLLAEPELLLKQ
IGNERSTFDEKEIARALHRYVDDPVDFANIRARLMASDDLVTLKAQVFDPETGKAAEPAVFTSRDMLRIE
YDMAQSARVLSQRKGFAVSSQAVAAAVETADPEKRFRLDAEQVDAVRHVTGESGIAAVVGLAGAGKSTLL
AAARVAWESDGRRVVGAALAGKAAEGLEDSSGIKSRTLASWELAWASGRNLLKRGNVLVIDEAGMVSSQQ
MARVLKAAEEAEAKVVLVGDAMQLQPIQAGAAFRAISERIGFAELAGVRRQREQWARSASRLFARGEVEK
GLDAYAQHGHLVEADTRDEVVGRMVADWTEARNRAIEASVSEGREGRLRGDELLVLAHTNEDVKRLNEAL
RSVMIDAGALSDRSSFRTERGEREFAAGDRIIFLENARFVEPRANSLGPQYVKNGMLGTVISTGDKRGDA
LLSVRLDNGRDVVISENSYRNVDHGYAATIHKSQGSTVDRTLVLATGMMDQHLTYVSMTRHRDGAEFYAA
KEDFEARPEWGWKPRADHAAGVTGELVETGNAKFRPDDEDADKSPYADVRTDAGTVHRLWGVSLPKALEK
AGISEGDTVTLRKDGVEKVKVQVTVVDEEAGEKRSEEREVDRNVWTAEQKESAAARSERIEKESHRPELF
GRLVERLSRSGAKTTTLDFESEEGYRAHAQDFARRRGLDTLSQAAAGMEEGASRRLAWVAEKRELVAKLW
ERASVALGFSIERERRAAYNEARAEALVEGMPVSGHYLIPPTTQFARGVDEDARLAQLSSPAWKDREAIL
QPLLEKIYRDPVAALSTLNALASDGDVEPRTLAGDLAAAPDRLGRLRGSDLVVDGRAARNERADAMAALR
ELLPLARAHATEFRRQAERFGIREQQRRAHMSLSIPMLSKPAMARLVEIERIRERGGDDAYKTAFAYAVE
DRQLVQEVKAVNDALTARFGWSAFTAKADVVAQRNIAERMPEDLAPERREKILRLFAAVRRFSEEQHLAE
KQDRSKIVAGASIEIGKEAMPMLPMFTAVTEFRTPVEEEARNRASTVAHYRHHRAALAETATLIWRDPAG
AVGKIEELVGKGFAGERIAAAVSNDPSAYGALRGSDRLMDRLLAVGRERKEAHQAVPKVASRVRSLGASW
ATALDAETRAVTEERRRMAVAIPGLSQAAEDALRKLVAEVNRQNKDKQKNTKRGVAAGSLEPRVVREFAE
VSRALDERFGRNAILRGEKDTGNLVSPAQRPAFEAMRERLQVLQQAVRAESTQNIIAERQRRTIERGRVF
TR
MAIMFVRAQVIGRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAAELVHEELALPDQIPAWFKNAVSG
KSVAGASEVLWNAVDAFETRADAQLARELIIALPEELTRAENIAVVREFVQDNFTSKGMVADWVYHDKDG
NPHIHLMMTLRPLTEEGFGPKKVAVLGEDGEPLRVVTPHRPNGKIVYKLWAGDKETMKVWKIAWADAANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGVEMYFAPADLARRQDMADRLLAEPELLLKQ
IGNERSTFDEKEIARALHRYVDDPVDFANIRARLMASDDLVTLKAQVFDPETGKAAEPAVFTSRDMLRIE
YDMAQSARVLSQRKGFAVSSQAVAAAVETADPEKRFRLDAEQVDAVRHVTGESGIAAVVGLAGAGKSTLL
AAARVAWESDGRRVVGAALAGKAAEGLEDSSGIKSRTLASWELAWASGRNLLKRGNVLVIDEAGMVSSQQ
MARVLKAAEEAEAKVVLVGDAMQLQPIQAGAAFRAISERIGFAELAGVRRQREQWARSASRLFARGEVEK
GLDAYAQHGHLVEADTRDEVVGRMVADWTEARNRAIEASVSEGREGRLRGDELLVLAHTNEDVKRLNEAL
RSVMIDAGALSDRSSFRTERGEREFAAGDRIIFLENARFVEPRANSLGPQYVKNGMLGTVISTGDKRGDA
LLSVRLDNGRDVVISENSYRNVDHGYAATIHKSQGSTVDRTLVLATGMMDQHLTYVSMTRHRDGAEFYAA
KEDFEARPEWGWKPRADHAAGVTGELVETGNAKFRPDDEDADKSPYADVRTDAGTVHRLWGVSLPKALEK
AGISEGDTVTLRKDGVEKVKVQVTVVDEEAGEKRSEEREVDRNVWTAEQKESAAARSERIEKESHRPELF
GRLVERLSRSGAKTTTLDFESEEGYRAHAQDFARRRGLDTLSQAAAGMEEGASRRLAWVAEKRELVAKLW
ERASVALGFSIERERRAAYNEARAEALVEGMPVSGHYLIPPTTQFARGVDEDARLAQLSSPAWKDREAIL
QPLLEKIYRDPVAALSTLNALASDGDVEPRTLAGDLAAAPDRLGRLRGSDLVVDGRAARNERADAMAALR
ELLPLARAHATEFRRQAERFGIREQQRRAHMSLSIPMLSKPAMARLVEIERIRERGGDDAYKTAFAYAVE
DRQLVQEVKAVNDALTARFGWSAFTAKADVVAQRNIAERMPEDLAPERREKILRLFAAVRRFSEEQHLAE
KQDRSKIVAGASIEIGKEAMPMLPMFTAVTEFRTPVEEEARNRASTVAHYRHHRAALAETATLIWRDPAG
AVGKIEELVGKGFAGERIAAAVSNDPSAYGALRGSDRLMDRLLAVGRERKEAHQAVPKVASRVRSLGASW
ATALDAETRAVTEERRRMAVAIPGLSQAAEDALRKLVAEVNRQNKDKQKNTKRGVAAGSLEPRVVREFAE
VSRALDERFGRNAILRGEKDTGNLVSPAQRPAFEAMRERLQVLQQAVRAESTQNIIAERQRRTIERGRVF
TR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 8448 | GenBank | WP_099086580 |
| Name | traG_FY154_RS23940_Yol001|pAt |
UniProt ID | _ |
| Length | 639 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 639 a.a. Molecular weight: 70585.34 Da Isoelectric Point: 9.3986
>WP_099086580.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MTIRARPHLSLLLILVPITVAAFAAYVVGWRWPELAAGMSGKTQYWFLRASPVPVLLFGPLAGLLTVWAL
PLHRRKPIAMATLICFLSVASFYGLREFGRLSPSVESGAATWNQALSFIDMVAVVGAVAGFMATAASARI
STVVSEPVKRARRGTFGDADWLSMSAAARLFPDDGEIVVGERYRVDKEIVHELPFDPNDPATWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVIPTALRYSGPLICLDPSTEVAPMVVEHRRERLGRQVMVLDPT
NPIMGFNVLDGIETSKQKEQDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLRQIVSEPETSVLAMLRDVQQNSASKFISETLGVFVNMTEQTFSGVYSTASKDTQWLSLDNYAALVC
GNTFRASDLIGGKKDVFLNIPASILRSYPGIGRVIVGSLINAMIEADGAFERRALFMLDEVDLLGYMRVL
EEARDRGRKYGVSMMLLYQSVGQLERHFGKDGAVSWIDGCAFASYAAIKALETARNVSAQCGEMTVEVKG
SSRNIGWDTKNSASRKSESVNFQRRPLIMPHEITQSMRKDEQIIVVQGHSPIRCGRAIYFRRKDMDTQVK
PNRFAKLRP
MTIRARPHLSLLLILVPITVAAFAAYVVGWRWPELAAGMSGKTQYWFLRASPVPVLLFGPLAGLLTVWAL
PLHRRKPIAMATLICFLSVASFYGLREFGRLSPSVESGAATWNQALSFIDMVAVVGAVAGFMATAASARI
STVVSEPVKRARRGTFGDADWLSMSAAARLFPDDGEIVVGERYRVDKEIVHELPFDPNDPATWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVIPTALRYSGPLICLDPSTEVAPMVVEHRRERLGRQVMVLDPT
NPIMGFNVLDGIETSKQKEQDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLRQIVSEPETSVLAMLRDVQQNSASKFISETLGVFVNMTEQTFSGVYSTASKDTQWLSLDNYAALVC
GNTFRASDLIGGKKDVFLNIPASILRSYPGIGRVIVGSLINAMIEADGAFERRALFMLDEVDLLGYMRVL
EEARDRGRKYGVSMMLLYQSVGQLERHFGKDGAVSWIDGCAFASYAAIKALETARNVSAQCGEMTVEVKG
SSRNIGWDTKNSASRKSESVNFQRRPLIMPHEITQSMRKDEQIIVVQGHSPIRCGRAIYFRRKDMDTQVK
PNRFAKLRP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 72552..82134
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| FY154_RS23720 (FY154_23545) | 68120..68596 | + | 477 | WP_099086617 | Hsp20 family protein | - |
| FY154_RS23725 (FY154_23550) | 68669..68968 | + | 300 | WP_099086616 | DUF982 domain-containing protein | - |
| FY154_RS23730 (FY154_23555) | 68979..69254 | + | 276 | WP_099086615 | hypothetical protein | - |
| FY154_RS23735 | 69266..69420 | - | 155 | Protein_70 | ATP-dependent DNA ligase | - |
| FY154_RS23740 (FY154_23560) | 69488..69727 | - | 240 | WP_099086614 | hypothetical protein | - |
| FY154_RS23745 (FY154_23565) | 69910..70248 | - | 339 | WP_144030956 | hypothetical protein | - |
| FY154_RS23750 (FY154_23570) | 70569..70811 | + | 243 | WP_144030955 | hypothetical protein | - |
| FY154_RS23755 (FY154_23575) | 71554..71916 | - | 363 | WP_099086612 | transcriptional regulator | - |
| FY154_RS23760 (FY154_23580) | 72010..72549 | + | 540 | WP_099086611 | hypothetical protein | - |
| FY154_RS23765 (FY154_23585) | 72552..73238 | + | 687 | WP_099086610 | lytic transglycosylase domain-containing protein | virB1 |
| FY154_RS23770 (FY154_23590) | 73235..73534 | + | 300 | WP_099086609 | TrbC/VirB2 family protein | virB2 |
| FY154_RS23775 (FY154_23595) | 73537..73878 | + | 342 | WP_099086608 | type IV secretion system protein VirB3 | virB3 |
| FY154_RS23780 (FY154_23600) | 73871..76252 | + | 2382 | WP_099086607 | VirB4 family type IV secretion system protein | virb4 |
| FY154_RS23785 (FY154_23605) | 76252..76950 | + | 699 | WP_099086606 | P-type DNA transfer protein VirB5 | virB5 |
| FY154_RS23790 (FY154_23610) | 76947..77180 | + | 234 | WP_099086605 | EexN family lipoprotein | - |
| FY154_RS23795 (FY154_23615) | 77185..78120 | + | 936 | WP_099086604 | type IV secretion system protein | virB6 |
| FY154_RS23800 (FY154_23620) | 78156..78422 | + | 267 | WP_099086603 | hypothetical protein | - |
| FY154_RS23805 (FY154_23625) | 78426..79097 | + | 672 | WP_099086602 | virB8 family protein | virB8 |
| FY154_RS23810 (FY154_23630) | 79097..79945 | + | 849 | WP_099086733 | P-type conjugative transfer protein VirB9 | virB9 |
| FY154_RS23815 (FY154_23635) | 79955..81124 | + | 1170 | WP_099086601 | type IV secretion system protein VirB10 | virB10 |
| FY154_RS23820 (FY154_23640) | 81133..82134 | + | 1002 | WP_099086600 | P-type DNA transfer ATPase VirB11 | virB11 |
| FY154_RS23825 (FY154_23645) | 82191..82535 | - | 345 | WP_099086599 | hypothetical protein | - |
| FY154_RS23830 (FY154_23650) | 83008..85155 | + | 2148 | WP_099086598 | ParB/RepB/Spo0J family partition protein | - |
| FY154_RS23835 (FY154_23655) | 85224..85880 | + | 657 | WP_099086597 | hypothetical protein | - |
| FY154_RS23840 (FY154_23660) | 86079..86501 | + | 423 | WP_099086596 | antirestriction protein | - |
Host bacterium
| ID | 11802 | GenBank | NZ_CP048479 |
| Plasmid name | Yol001|pAt | Incompatibility group | - |
| Plasmid size | 386412 bp | Coordinate of oriT [Strand] | 106514..106542 [+] |
| Host baterium | Agrobacterium tumefaciens strain Yol001 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | bphC |
| Symbiosis gene | - |
| Anti-CRISPR | - |