oriTDB

The information of the oriT region

oriTDB accession number	100093
Name	oriT_pRiA4b
Sequence Completeness	core
oriT length	38 nt
oriT sequence	CCAAGGGCGCAATTATACGTCGCTGGCGCGACGTGTTG
IR (inverted repeat)	[15-23] [28-36] nt (ATACGTCGC..GCGACGTGT)
Location of nic site	[7-8] nt
Conserved sequence flanking the nic site	AGGG\|CGCA
Note	Ri plasmid
	L:15-23;R:28-36;D:7-8

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	88
Name	TraA_pRiA4b
GenBank accession number	BAB47249
Family	MOB_Q
Length	1108 aa
UniProt ID	Q93UY4
PDB ID	_
Pfam	MobA_MobL [PF03389.14], Evalue: 3.40E-77, Aligned region: 17..243 AAA_30 [PF13604.5], Evalue: 4.00E-58, Aligned region: 386..573 AAA_19 [PF13245.5], Evalue: 1.20E-11, Aligned region: 391..518 Viral_helicase1 [PF01443.17], Evalue: 9.30E-05, Aligned region: 666..742 UvrD_C_2 [PF13538.5], Evalue: 1.50E-06, Aligned region: 697..741
Note	relaxase
Protein sequence [Download]	MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAP EWVRSMIADRSVAGASEAFWNKVEAFEKRSDAQLAKDVTIALPIELTAEQNIALMRDFVE RHITSKGMVADWVYHDAPGNPHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIV YDLWAGSTEEFNAFRDGWFACQNKHLALAGLDIRIDGRSFEKQGIDLEPTIHLGVGAKAI ERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPEIVLELITREKSVFDERDVAK VLYRYIDDVALFQSLMVRILQSPVALRLERERIDFATGIRTPAKYTTREMIRLEAEMANR AIWLSGRASHGVREAVLEATFARHVRLSDEQRTAIEHVADGERIAAIIGRAGAGKTTMMK AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNQLDDKTIIVLD EAGMVSSRQMALLVETVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQ RQQWMRDASLDLARGNVRKAVDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLIL AHLRRDVRMLNEMARAKLVERGIVANGFAFKTEDGTRMFAAGDQIVFLKNEGSLGVKNGM LAKVLEAALGRIVAEIGEGEHRRKVTIEQRFYNNLDHGYATTIHKSQGATVDRVKVLASL SLDRHLTYVAMTRHREDLAVYYGSRSFAKSGDLVPILSRRNAKETTLDYEKASFYGQALR FADTRGLHLMDVARTVARDRLEWTIRQSSRLVDLGVRLAAIATKLGFVGSFKNSPIQNPI KEAKPMVSGITTFPKSLEQAVEDKLAADPGLKKQWEDVSTRFHLVYAQPEAAFKAINVDT MLKDQSVAQSTLARIAGEPESFGALKGKTGVLASRADRQDREKAIANVPALARNLERYLR ERAEAEFKHETEERAVRLKVSVDIPALSPSAKQTLERVRDAIDRNDLPAGLEYALADKMV KAELEGFAKAVSERFGERTFLPLAAKDTDGKTFETATAGMTAGQKAEVQSAWNSMRTVQQ LAAHERTTEALKQAETLRQTKSQGLSLK

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]

II. Auxiliary DNA-binding protein(s) of the relaxosome

#	ID	Name	GenBank	Length	Note
1	127	TraC_pRiA4b	BAB47248	97 aa	conjugal transfer protein TraC
2	128	TraD_pRiA4b	BAB47247	71 aa	conjugal transfer protein TraD

Information of T4CP

ID	88
Name	TraG_pRiA4b
SecReT4 accesion number	_
GenBank accession number	BAB47246
Family	VirD4/TraG
Length	652
UniProt ID	Q93UY7
PDB ID	_
Pfam	T4SS-DNA_transf [PF02534.13], Evalue: 2.40E-158, Aligned region: 163..641 TraG-D_C [PF12696.6], Evalue: 2.30E-34, Aligned region: 477..599 TrwB_AAD_bind [PF10412.8], Evalue: 2.30E-20, Aligned region: 225..613
Note	conjugal transfer coupling protein TraG
Protein sequence [Download]	MTVSRIALVAGPAALMILVVIGMTGIEQWLSDFGKTGAARLTWGRVGIALPYVVSSAIGI LFLFASAGSINIKQAGWGALTGCTATILIAAIRETTRLGAFMKVLPADKTILAYLDPATS IGASAALLCACFALRVALIGNAAFASAKPKRIHGKRALHGEADWMKLTEAATLFSDAGGI VIGERYRVDKDNVAAQAFRADNAETWGAGGKSPLLCFNGSFGSSHGIVFAGSGGFKTTSV TIPTALKWGSTLIVLDPSNEVAPMVSAHRGGAGRDVFVLDPKKPDIGFNVLDWVGRFGGT KEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDETEQTLRQVRM NLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA ALVSGRKFSTSDIAGGNTDVFINIDLKTLETHSGLARVVIGSLLNAIYNRDGQLEGRALF LLDEVARLGYMRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDASSKWFESASWISF AAINDPETADYISKRCGMTTVEIDQVSRSSQARGSSRTRSKQLAARPLIQPHEVLRMRAD EQIVFTAGNAPLRCGRAMWFRREAMKACVGKNRFHGTRDPDATAQKAATRRL

Reference
N/A

Information of plasmid

ID	88
Plasmid name	pRiA4b
GenBank accession number	AB050904.1
Genome size	30000 bp
Coordinate of oriT [Strand]	9988..10025 [-]
Drug resistance	_
Heavy-metal resistance	_
Virulence factor	virulence-rhizogenic
Xenobiotic degradation	_
Host bacterium [NCBI Taxonomy ID]	Agrobacterium tumefaciens A4 [358]

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]