oriTDB
The information of the oriT region
oriTDB accession number 100077
Name oriT_pRi1724  insolico
Sequence Completeness core
oriT length 32 nt
oriT sequence AGGGCGCAATTATACGTCGCTGATGCGACGCC
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
L:15-20;R:25-30;D:4-5
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]
I. Information of Relaxase
ID 72
Name TraA_pRi1724 insolico
GenBank accession number NP_066693
Family MOBQ
Length 1108 aa
UniProt ID Q9F5E0
PDB ID _
Pfam MobA_MobL [PF03389.14], Evalue: 2.10E-75, Aligned region: 17..243
AAA_30 [PF13604.5], Evalue: 1.70E-57, Aligned region: 386..573
AAA_19 [PF13245.5], Evalue: 2.60E-11, Aligned region: 391..518
Viral_helicase1 [PF01443.17], Evalue: 0.00013, Aligned region: 671..742
UvrD_C_2 [PF13538.5], Evalue: 1.50E-06, Aligned region: 697..741
Note Dtr system oriT relaxase; Provisional
Protein sequence [Download] MAVPHFSVSIVARGSGRSVVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADSP
EWLRSMIADRSVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPLELTSEQNIALMRDFVE
RHITSKGMVADWVYHDAPGNPHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIV
YELWAGSTEDFNAFRDGWFACQNKHLALAGLDIRIDGRSFETQGIDLEPTIHLGVGTKAI
ERKAGQTDRTSETSAPKLERIEIQEARRSENARRIQRRPEIVLELITREKSVFDERDVAK
VLYRYIDDARLFQSLMVRILQSPEALRLERERLNFATGIRTPAKYTTREMIRLEAEMANR
AIWLSARASHGVREAVLQATFERHARLSGEQRTAIEHVVGGERIAAIIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNQLDNKTIIVLD
EAGMVSSRQMALLVETVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRVGYAELETIYRQ
RQQWMRDASLDLARGNVRKAVDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLIL
AHLRRDVRMLNEMARAKLVERGVVAAGFAFKTEQGIRMFAAGDQIVFLKNEGSLGVKNGM
LAKVLEAAPGRIVAEIGDAEHRRQVTIEQRFYDNLDHGYATTIHKSQGATVDRVKVLASL
SLDRHLTYVAMTRHREDLAVYYGSRSFAKAGGLIPILSRRNAKETTLDYDKASFYGQALR
FAEARGMHLMNVARTVARDRLEWTIRQSSRLVDLGVRLAAIATKLGFVGSFKNSPIQNPI
KEAKPMVSGITTFPKSFEQAVEDKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKAINVDA
MIKDQSVAQSTLTRIADAPESFGALKGKTGLLASRAEKQDREKAVANVPALARNLERYLR
ERAEAELKHEMEERAVRLKVSVDIPALSPAARQTLERVRDAIDRNDLPAGLEYALADKMV
KAELEGFAKAVSERFGERTFLPLAAKDTSGKTFETVTAGMTAGQKAEVQSAWNSMRTIQQ
LAAHERTTEALKQAETLRQTKSQGLSLK
Reference
 N/A

II. Auxiliary DNA-binding protein(s) of the relaxosome
# ID Name GenBank Length Note
1 104 TraC_pRi1724 insolico NP_066692 97 aa conjugal transfer protein TraC; Provisional
2 105 TraD_pRi1724 insolico NP_066691 71 aa conjugal transfer protein TraD; Provisional
Information of T4CP
ID 72
Name TraG_pRi1724 insolico
SecReT4 accesion number 10954755
GenBank accession number NP_066690
Family VirD4/TraG
Length 667
UniProt ID Q9F5E3
PDB ID _
Pfam T4SS-DNA_transf [PF02534.13], Evalue: 3.00E-154, Aligned region: 163..642
TraG-D_C [PF12696.6], Evalue: 5.30E-35, Aligned region: 477..599
TrwB_AAD_bind [PF10412.8], Evalue: 3.60E-20, Aligned region: 227..613
Note conjugal transfer coupling protein TraG
Protein sequence [Download] MTINRIALVVGPAALMILVIIGMTGIEQWLSGFGKTEAARLAWGRAGIALPYIASAAIGV
LFLFASAGSINIKQAGWGVLAGCSGTILIAATRETMRLAAFTKALPADKTIFAYLDPATS
IGAGAAFMCACFAFRVVLIGNAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDSGGI
VVGERYLVDKDSVGSQAFRADNAETWGAGGKSTLLCFDGSFGSSHGIVFAGSGGFKTTSV
TIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDMFVLDPRKSDIGFNVLDWVGGYGGT
KEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDEKDQTLRQVRM
NLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVVIGSLLNAIYNRDGKLEGRALF
LLDEVARLGYMRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISF
AAINDPETADYISKRCGMTTVEIDQDSRSSQARGSSRTRSKQLAARPLIQPHEVLRMRAD
EQIVFTAGNAPLRCGRAIWFRRADMRVCVGENRFHSTGGGEKKASNSTPSVKADETTPTV
RSAGEEG

Reference
 N/A
Information of plasmid
ID 72
Plasmid name pRi1724
GenBank accession number NC_002575.1
Genome size 217594 bp
Coordinate of oriT  [Strand] 140057..140088 [+]
Drug resistance _
Heavy-metal resistance _
Virulence factor experimental virulence-rhizogenic
Xenobiotic degradation _
Host bacterium [NCBI Taxonomy ID] Agrobacterium rhizogenes MAFF03-01724 [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]

Microbial Bioinformatics Group in MML, SJTU