 oriTDB accession number | 100029 |
| Name | oriT_pRi2659  |
Sequence Completeness  | core |
| oriT length | 32 nt |
| oriT sequence | AGGGCGCAATTATACGTCGCTCACGCGACGCC |
| IR (inverted repeat) | [15-20] [25-30] nt (CGTCGC..GCGACG) |
| Location of nic site | [4-5] nt |
| Conserved sequence flanking the nic site | AGGG|CGCA |
| Note | Ri plasmid |
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] |
| ID | 28 |
| Name | TraA_pRi2659 |
| GenBank accession number | YP_001961052 |
| Family | MOBQ |
| Length | 1109 aa |
| UniProt ID | A8W094 |
| PDB ID | _ |
| Pfam | MobA_MobL [PF03389.14], Evalue: 2.70E-76, Aligned region: 17..243 AAA_30 [PF13604.5], Evalue: 1.10E-59, Aligned region: 386..573 AAA_19 [PF13245.5], Evalue: 2.70E-13, Aligned region: 391..518 Viral_helicase1 [PF01443.17], Evalue: 8.90E-05, Aligned region: 662..742 AAA_22 [PF13401.5], Evalue: 7.80E-07, Aligned region: 396..516 UvrD_C_2 [PF13538.5], Evalue: 1.50E-06, Aligned region: 697..741 |
| Note | Dtr system oriT relaxase |
| Protein sequence [Download] | MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKLGLLHEEFVIPADSP EWVRSMIADRSVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPLELTSEQNIALMRDFVE RHITAKGMVADWVYHDAPGNPHVHLMTTLRPLTEDGFGSKKVAVLGRDGKPIRNDAGKIV YDLWAGSTEDFNAFRDGWFACQNKHLALAGLDIRIDGRSFEKQGIDLEPTIHLGVGAKAI ERKAEQSDGKQETAPPKLERIELQEARRSENARRIQRRPEIVLELITREKSVFDERDVAK VLYRYIDDARLFQSLMVRILQSPEALRLERERMNLATGVRELAKYTTREMIRLEAEMANR AIWLSARASHGVREAVLQATFARHSRLSDEQRTAIEHVAGGERIAAVIGRAGAGKTTMMK AAREAWEAAGYRVVGIALAGKAAEGLEKEAGIPSRTLSSWELRWNQGRNQLDNKTVIVLD EAGMVSSRQMALLVETVTKAGAKLVLVGDPEQLQPIEAGAAFRAIAARIGYAELETIYRQ RQQWMRDASLDLARGNIRKAVDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLIL AHLRRDVRMLNDMARAKLVERGVVAEGFAFKTEDGHRKFAPGDQIVFLKNEGSLGVKNGM LAKVLKAAPGRVVAEVGEGEHRRQVTIEQRFYNNLDHGYATTIHKSQGATVDRVKVLASL SLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYEQASFYRQALR FAEARGLHLMNVARAVARDRLEWTIRQKQKLVGLGARLAAIATKLGFVGNFKNSPIQNPI KEAKPMVSGITTFPKSFEQAVEDKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKAINVDA MVKDQSVAKSTLAKVADAPESFGTLKGKPGLLASRAEKQDREKAIANVPALGRNLERYLR ERAEAELKHETEERAVRLKVSVDIPALSPAAKQMLERVRDAIDRNDLPAGLEYALADKMV KAELEGFAKAVSERFGERTFLPLAAKDTNGKAFETVTAGMTAGQKAEVQSAWNSMRTVQQ LAAHERTTEALKQAETLRQTKSQGLSLK |
Reference| # | ID | Name | GenBank | Length | Note |
| 1 | 42 | TraC_pRi2659 | YP_001961051 | 102 aa | probable traC gene, Ti plasmid conjugal DNA processing; similar to riorf111 in pRi1724 |
| 2 | 43 | TraD_pRi2659 | YP_001961050 | 71 aa | probable traD gene, conjugal transfer protein similar to riorf110 in pRi1724 |
| ID | 28 |
| Name | TraG_pRi2659 |
| SecReT4 accesion number | 190404418 |
| GenBank accession number | YP_001961049 |
| Family | VirD4/TraG |
| Length | 667 |
| UniProt ID | A8W087 |
| PDB ID | _ |
| Pfam | T4SS-DNA_transf [PF02534.13], Evalue: 4.60E-157, Aligned region: 163..641 TraG-D_C [PF12696.6], Evalue: 8.40E-35, Aligned region: 477..599 TrwB_AAD_bind [PF10412.8], Evalue: 1.90E-20, Aligned region: 224..613 |
| Note | conjugal transfer coupling protein TraG |
| Protein sequence [Download] | MTINRIALVVGPAALMILVVIGMTGIEQWISGFGKTEAARLAWGRAGIALPYVASAAIGI VFLFASAGAISIKQAGWGVVAGCSGTILIAATRETIRLAAFTKTLPTGKTVFAYLDPATS IGVGAAFMCACFALRVAFIGNAAFARAEPKRIQGKRALHGEADWMKPPEAAKLFSDSGGI VIGERYRVDKDSVAALAFRADSAETWGAGGKSPLLCFDGSFGSSHGIVFAGSGGFKTTSV TIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLDPRKSDMGFNVLDWVGRFGGT KEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHMDEKDQTLRRVRM NLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA ALVSGRKFSTSDIAAGNTDVFINIDLKTLETHSGLARVVIGSLLNAIYNRDGKLEGRALF LLDEVARLGYMRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISF AAINDPETADYISKRCGMTTVEIDQVSRSSQARGSSRTRSKQLAARPLIQPHEVLRMRAD EQIVFTAGNAPLRCGRAIWFRRNDMRACVGENRFHSMGGREKEGSNSASAVNAYETKPAV TSAAEEE |
Reference| ID | 28 |
| Plasmid name | pRi2659 |
| GenBank accession number | NC_010841.1 |
| Genome size | 185462 bp |
| Coordinate of oriT [Strand] | 106646..106677 [+] |
| Drug resistance | _ |
| Heavy-metal resistance | _ |
| Virulence factor |  virulence-rhizogenic T-DNA processing virulence virA/G regulated protein |
| Xenobiotic degradation | _ |
| Host bacterium [NCBI Taxonomy ID] | Agrobacterium rhizogenes K599 [359] |
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] |