Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100035 |
| Name | oriT_pAoF64/95  |
| Organism | Agrobacterium tumefaciens strain F64/95 |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | JX683454 (156581..156619 [+], 39 nt) |
| oriT length | 39 nt |
| IRs (inverted repeats) | 17..23, 28..34 (ACGTCGC..GCGACGT) |
| Location of nic site | 7..8 |
| Conserved sequence flanking the nic site |
_ |
| Note | similar to oriT regions of pTiC58 |
oriT sequence
Download Length: 39 nt
>oriT_pAoF64/95
CCAAGGGCGCAATTATACGTCGCTGGCGCGACGTGTTGC
CCAAGGGCGCAATTATACGTCGCTGGCGCGACGTGTTGC
Visualization of oriT structure
Reference
[1] Wetzel ME et al. (2015) The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups. Genome Biol Evol. 7(12):3337-57. [PMID:26590210]
[2] Wetzel ME et al. (2014) Quorum-dependent mannopine-inducible conjugative transfer of an Agrobacterium opine-catabolic plasmid. J Bacteriol. 196(5):1031-44. [PMID:24363349]
Relaxase
| ID | 34 | GenBank | AFX65723 |
| Name | TraA_pAoF64/95 |
UniProt ID | K7X7S1 |
| Length | 1108 a.a. | PDB ID | |
| Note | be responsible for nicking the oriT | ||
Relaxase protein sequence
Download Length: 1108 a.a. Molecular weight: 123029.22 Da Isoelectric Point: 9.7328
>AFX65723.1 Conjugative transfer protein TraA (plasmid) [Agrobacterium radiobacter]
MAVPHFSVSILARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVIPADAPDWVRSMIADR
SVAGASETFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAQGMVADWVYHDVPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLQATFARHSRLSDEQRTAIEHVAGAPRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSWQM
ALFVEAVTKVRAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVGSLIAAWDRDYDPSKISLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFAPGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEVGEGERRQQVTVEQRFYNNLDHGYA
TTIHKSQGATVDQVKVLASLSLDRHLTYVAMTRHREDLAVYYGTRSFAKSGGLIAILSRRNAKETTLDYE
KSALYRQALRFAEARGLHLMNVARTIAHDRLQWAVRQSSRLADLGARLAAIGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAIDVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGLLASRGDKQDREKAIANAPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPSAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETATAGMTAGQKAEVQSAWNSMRTVQQLAAHERTTEALKQAETLRQTKSQGLSLK
MAVPHFSVSILARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVIPADAPDWVRSMIADR
SVAGASETFWNKVEGFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAQGMVADWVYHDVPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASHGVREAVLQATFARHSRLSDEQRTAIEHVAGAPRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSWQM
ALFVEAVTKVRAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVGSLIAAWDRDYDPSKISLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFAPGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEVGEGERRQQVTVEQRFYNNLDHGYA
TTIHKSQGATVDQVKVLASLSLDRHLTYVAMTRHREDLAVYYGTRSFAKSGGLIAILSRRNAKETTLDYE
KSALYRQALRFAEARGLHLMNVARTIAHDRLQWAVRQSSRLADLGARLAAIGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAKPEAAFKAIDVDTMLKDQSVAQS
TLARIAGEPESFGALKGKTGLLASRGDKQDREKAIANAPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPSAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETATAGMTAGQKAEVQSAWNSMRTVQQLAAHERTTEALKQAETLRQTKSQGLSLK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | K7X7S1 |
Auxiliary protein
| ID | 51 | GenBank | AFX65722 |
| Name | TraC_pAoF64/95 |
UniProt ID | K7WTA3 |
| Length | 98 a.a. | PDB ID | _ |
| Note | Conjugative transfer protein TraC | ||
Auxiliary protein sequence
Download Length: 98 a.a. Molecular weight: 10000.15 Da Isoelectric Point: 6.3845
>AFX65722.1 Conjugative transfer protein TraC (plasmid) [Agrobacterium radiobacter]
MKKPSAKIRDEIAKLQEQLKIAETREAERIGRIALKAGLGEIEIDEAELQAAFEQLTKRFRGGQGATTAG
KKGAGDSSGQASTAADASGAGAGSAGEA
MKKPSAKIRDEIAKLQEQLKIAETREAERIGRIALKAGLGEIEIDEAELQAAFEQLTKRFRGGQGATTAG
KKGAGDSSGQASTAADASGAGAGSAGEA
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | K7WTA3 |
| ID | 52 | GenBank | AFX65721 |
| Name | TraD_pAoF64/95 |
UniProt ID | K7XK84 |
| Length | 71 a.a. | PDB ID | _ |
| Note | Conjugative transfer protein TraD | ||
Auxiliary protein sequence
Download Length: 71 a.a. Molecular weight: 7832.98 Da Isoelectric Point: 10.2652
>AFX65721.1 Conjugative transfer protein TraD (plasmid) [Agrobacterium radiobacter]
MARTMTSDARKKDTREKIELGGLIVKSGLRYEKRALLLGALLDAARRIKGDEGERSRLTAIGVEAFGNDD
Q
MARTMTSDARKKDTREKIELGGLIVKSGLRYEKRALLLGALLDAARRIKGDEGERSRLTAIGVEAFGNDD
Q
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | K7XK84 |
T4CP
| ID | 34 | GenBank | AFX65720 |
| Name | TraG_pAoF64/95 |
UniProt ID | K7WNC6 |
| Length | 644 a.a. | PDB ID | _ |
| Note | Conjugative transfer coupling protein TraG | ||
T4CP protein sequence
Download Length: 644 a.a. Molecular weight: 69543.66 Da Isoelectric Point: 8.8914
>AFX65720.1 Conjugative transfer coupling protein TraG (plasmid) [Agrobacterium radiobacter]
MTINRIALVVVPGTLMILVVVGMTGIEQWLSGFGKTEAARLAWGRVGIALPYGASAAIGILFLFSSAGSI
NIRQAGWGVVAGSSGTISIAALRETVRLSAFMKAMPTDNTVLAYLDPATAIGAGVLLMCACFALRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDTGGIVIGEHYRVDKDSVASQAFRSDNAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGSTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PKKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
TEQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDIFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQMKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRLRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMIGDAPKPA
MTINRIALVVVPGTLMILVVVGMTGIEQWLSGFGKTEAARLAWGRVGIALPYGASAAIGILFLFSSAGSI
NIRQAGWGVVAGSSGTISIAALRETVRLSAFMKAMPTDNTVLAYLDPATAIGAGVLLMCACFALRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDTGGIVIGEHYRVDKDSVASQAFRSDNAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGSTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PKKPDIGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
TEQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDIFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQMKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISKRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRLRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMIGDAPKPA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 161749..175550
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_159 | 160016..160579 | + | 564 | AFX65724 | Putative conjugative transfer pilin processing protease TraF | - |
| Locus_160 | 160569..161732 | + | 1164 | AFX65725 | Conjugative transfer protein TraB | - |
| Locus_161 | 161749..162363 | + | 615 | AFX65726 | Conjugative transfer protein TraH | virB1 |
| Locus_162 | 162569..164149 | + | 1581 | AFX65727 | Putative FIC/DOC family protein | - |
| Locus_163 | 164195..164425 | - | 231 | AFX65728 | Positive regulatory element in transfer | - |
| Locus_164 | 164639..164962 | + | 324 | AFX65729 | Antiactivator of conjugative transfer | - |
| Locus_165 | 164965..165669 | - | 705 | AFX65730 | LuxR-type activator protein | - |
| Locus_166 | 166019..167317 | - | 1299 | AFX65731 | Conjugative transfer protein TrbI | virB10 |
| Locus_167 | 167329..167775 | - | 447 | AFX65732 | Conjugative transfer protein TrbH | - |
| Locus_168 | 167779..168594 | - | 816 | AFX65733 | Conjugative transfer protein TrbG | virB9 |
| Locus_169 | 168611..169273 | - | 663 | AFX65734 | Conjugative transfer protein TrbF | virB8 |
| Locus_170 | 169294..170475 | - | 1182 | AFX65735 | Conjugative transfer protein TrbL | virB6 |
| Locus_171 | 170469..170672 | - | 204 | AFX65736 | Conjugative transfer protein TrbK | - |
| Locus_172 | 170666..171469 | - | 804 | AFX65737 | Conjugative transfer protein TrbJ | virB5 |
| Locus_173 | 171441..173897 | - | 2457 | AFX65738 | Conjugative transfer protein TrbE | virb4 |
| Locus_174 | 173908..174207 | - | 300 | AFX65739 | Conjugative transfer protein TrbD | virB3 |
| Locus_175 | 174200..174583 | - | 384 | AFX65740 | Conjugative transfer protein TrbC | virB2 |
| Locus_176 | 174573..175550 | - | 978 | AFX65741 | Conjugative transfer protein TrbB | virB11 |
| Locus_177 | 175562..176185 | - | 624 | AFX65742 | Acyl-homoserine-lactone synthase | - |
Host bacterium
| ID | 34 | GenBank | JX683454 |
| Plasmid name | pAoF64/95 | Incompatibility group | _ |
| Plasmid size | 176574 bp | Coordinate of oriT [Strand] | 156581..156619 [+] |
| Host baterium | Agrobacterium tumefaciens strain F64/95 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |