Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 107577
• Name: oriT_pRlvD
• Organism: Rhizobium leguminosarum bv. viciae strain UPM791
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP025510 (120599..120632 [-], 34 nt)
• oriT length: 34 nt
• IRs (inverted repeats): 19..24, 29..34 (CGTCGC..GCGACG)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 34 nt

>oriT_pRlvD
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traA_RLV_RS37660_pRlvD

• ID: 5091
• GenBank: WP_104891287
• Name: traA_RLV_RS37660_pRlvD
• UniProt ID: _
• Length: 1108 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1108 a.a.
• Molecular weight: 122922.11 Da
• Isoelectric Point: 9.6646

>WP_104891287.1 Ti-type conjugative transfer relaxase TraA [Rhizobium leguminosarum]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADR
SVAGASEAFWNKVEGFEKRSDAQLAKDVTIALPLELTAEHNIALMRDFVERHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYELWAGSTEDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERVELQEQRRSENARRIQHRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMVRILQSPEALRLERERINFAMGIRTPEKYTTRDM
IRLEAQMANRAIWLSARATHGVREAVLQATFARHSRLSDEQRTAIEHITGATRIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLGDRCVFVLDEAGMVSSRQM
ALFVEAVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMLGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFATGDQVVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEVGEGEHRRQVTVEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLAYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETSLDYE
KSALYRQALRFAEARGLHLMNVARTIAHDRLQWAVRQSSRLADLGARLAAIGKALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYANPEAAFKAIDVDTMLKDQSVAQS
TLARIAGEPEGFGALKGKTGLLASRADKQDLEKAVANVPALARNLERYLRERAEAELKHQTEERAVRLKV
SVDIPALSPSAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTAGQKAEVRNAWDAMRAVQQLAAHERTTEALKQAETLRQTTSQGLSLK

Protein domains

Predicted by InterproScan.

• AAA domain (AAA_30) (387-569)

• Viral (Superfamily 1) RNA helicase (Viral_helicase1) (696-740)

• BID domain of Bartonella effector protein (Bep) (Bep_C_terminal) (864-960)

• MobA/MobL family (MobA_MobL) (17-243)

Protein structure

No available structure.

T4CP

t4cp2_RLV_RS37520_pRlvD

• ID: 5304
• GenBank: WP_245461641
• Name: t4cp2_RLV_RS37520_pRlvD
• UniProt ID: _
• Length: 541 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 541 a.a.
• Molecular weight: 59676.47 Da
• Isoelectric Point: 5.1482

>WP_245461641.1 DUF87 domain-containing protein [Rhizobium leguminosarum]
MVSVKDYPAETYPGILDRLNLPYDTVVTQSFTPIDPISAQGKIARVRKQMRAAEDAAISLMAQLEEAEDD
VASGRVIFGDHHCSVAVFCDSLKELDGAMAYVARAMQDAGSAIVRENFSSRVVYFAQHPGNFAYRTRPAM
ISSQNFAQLCAMHGQSKGSPPDKCPWGDAVTIFPTARGETFRFNFHLPGKPGQRTVGHTLVLGQTGSGKT
LGTAFLISQAQRLGARTILFDKDNGFEMAVRAMGGRYSTVRMGDETGFNPIRAEADSRGAAWLTDWLAAL
AEYDGGKLNPLQIQALSDAVQANTSADPRLQNLEQFRSQLRATDDDGDLYNRLGRWDETGQFGWLFSGKG
LDPLAFDNRLTAFDLTEVFDNDVVRTAWLSYVFRRVERLVEDEHPTLLVLDEAWKLLDDPYFEARLKDWM
LTMRKKNVAVVLLTQRVSHITNSAAGDAILESAVTRLVYTSSFNTAAELAPLHLTPTESAFLQMSNVDNH
LVLLKSGSDSVVLDFDLVAIGKGIDVLGGGRGEKAIAGWRDRPDFQMEMLQ

Protein domains

Predicted by InterproScan.

• TraG P-loop domain (P-loop_TraG) (188-458)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (1-137)

Protein structure

No available structure.

virD4_RLV_RS37870_pRlvD

• ID: 5305
• GenBank: WP_165505212
• Name: virD4_RLV_RS37870_pRlvD
• UniProt ID: _
• Length: 606 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 606 a.a.
• Molecular weight: 67296.23 Da
• Isoelectric Point: 7.8571

>WP_165505212.1 MULTISPECIES: type IV secretion system ATPase VirD4 [Rhizobium]
MDGSTTRKLNTLLFAFLLSLTVGLLFASIYASFYRHGISRETTNRFDIFSFWYETPLYVGYATPVFLRGL
TIAVSTAVLATMAGAIVILRKPHHHGTARWAARQELQRAGYIRPFRNITGPIFGKTVGPRWPGRYLTNGE
QPHSLVVAPTRAGKGVGVVIPTLLTFNGSILALDVKGELFELTSRARVTRGDRVFKFAPLDSAGRTHSYN
PVLDIVNMSPERRFSETRRLAVNLIVAKGKGSEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGE
KYKLFAQLAEETQNQEAQRIFDNMASNDTKILTSYTSVLGDGGLNLWADPLIKAATTTSDFSIYDLRRDP
TSIFLCVSPNDLEVIAPLIRLFFQQVVSILQRTLPKKDEIFEVLFLLDEFKHLGKLEAIETAVTTIAGYK
GRFMFIIQSLSALTGAYEESGKENFLSNTGIQIFMATADDETPNYISKAIGDYTFRARSTSFSQRNIFDT
NIQLSDQGAPLLRPEQVRLIDDDMEIVLIKGQPPLRLKKLKYYSDRVLKRIFDRQSGALPEPEPLHFATT
YVQAPATLLVAAESLPDEAKLEDAVQAALPDFDEVPVEGQGRCHLV

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (99-540)

Protein structure

No available structure.

t4cp2_RLV_RS37960_pRlvD

• ID: 5306
• GenBank: WP_077988070
• Name: t4cp2_RLV_RS37960_pRlvD
• UniProt ID: _
• Length: 793 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 793 a.a.
• Molecular weight: 87501.45 Da
• Isoelectric Point: 6.2170

>WP_077988070.1 DUF87 domain-containing protein [Rhizobium leguminosarum]
MAKGWCTVLERLATRAARSLALKRSEKGEMLVSGLPYLSAVDDVTLMLRDGDLMGSFVVEGINAETGDSF
HTVELCNAFSRFIAQQRSDVAYYVHRISVETRPTMPPVHGHPFNEEIDRRWQGYLQMVGLRDRVTVVTLV
IRPPRKTAKFLSLFGGRDVHSRHEVEARALRLDQMINTCMVGVGEAGPSRLTVSDGRWLGLLRTLIDGSG
GSLIPGTKFLPVADLLASSQITFQGPVFECEGTDPGRRRFGTIVSVKDYPAETYPGILDRLNLPYDTVVT
QSFTPIDPISAQGKIARVRKQMRAAEDAAISLMAQLEEAEDDVASGRVIFGDHHCSVAVFCDSLKELDGA
MAYVARAMQDAGSAIVRENFSSRVVYFAQHPGNFAYRTRPAMISSQNFAQLCAMHGQSKGSPPDKCPWGD
AVTIFPTARGETFRFNFHLPGKPGQRTVGHTLVLGQTGSGKTLGTAFLISQAQRLGARTILFDKDNGFEM
AVRAMGGRYSTVRMGDETGFNPIRAEADSRGAAWLTDWLAALAEYDGGKLNPLQIQALSDAVQANTSADP
RLQNLEQFRSQLRATDDDGDLYNRLGRWDETGQFGWLFSGKGLDPLAFDNRLTAFDLTEVFDNDVVRTAW
LSYVFRRVERLVEDEHPTLLVLDEAWKLLDDPYFEARLKDWMLTMRKKNVAVVLLTQRVSHITNSAAGDA
ILESAVTRLVYTSSFNTAAELAPLHLTPTESAFLQMSNVDNHLVLLKSGSDSVVLDFDLVAIGKGIDVLG
GGRGEKAIAGWRDRPDFQMEMLQ

Protein domains

Predicted by InterproScan.

• TraG P-loop domain (P-loop_TraG) (440-710)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (201-389)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 82607..91785

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
RLV_RS37495 (RLV_2107)	77875..80563	-	2689	Protein_91	shikimate kinase	-
RLV_RS37500 (RLV_2108)	80569..81319	+	751	Protein_92	IS6 family transposase	-
RLV_RS39420 (RLV_2109)	81651..82484	+	834	WP_245461638	lytic transglycosylase domain-containing protein	-
RLV_RS37510 (RLV_2110)	82607..82918	+	312	WP_077988068	TrbC/VirB2 family protein	virB2
RLV_RS37515	83002..83280	+	279	WP_104891276	VirB3 family type IV secretion system protein	virB3
RLV_RS39425 (RLV_2111)	83339..84064	+	726	WP_245461639	hypothetical protein	virb4
RLV_RS37520 (RLV_2112)	84007..85632	+	1626	WP_245461641	DUF87 domain-containing protein	virb4
RLV_RS37525	85763..86566	+	804	WP_245315068	type IV secretion system protein	-
RLV_RS39430 (RLV_2114)	86607..87113	+	507	WP_245461640	hypothetical protein	virB6
RLV_RS39435	87077..87715	+	639	WP_245461642	type IV secretion system protein	virB6
RLV_RS37535 (RLV_2115)	87928..88602	+	675	WP_077988072	type IV secretion system protein	virB8
RLV_RS37540 (RLV_2116)	88630..89412	+	783	WP_077988073	TrbG/VirB9 family P-type conjugative transfer protein	virB9
RLV_RS37545 (RLV_2117)	89612..90787	+	1176	WP_104891313	TrbI/VirB10 family protein	virB10
RLV_RS37550 (RLV_2118)	90784..91785	+	1002	WP_104891277	P-type DNA transfer ATPase VirB11	virB11
RLV_RS38420	92046..92246	-	201	WP_131618399	hypothetical protein	-
RLV_RS37555 (RLV_2119)	92366..93088	+	723	WP_104891278	response regulator	-
RLV_RS37560 (RLV_2120)	93247..93999	+	753	WP_104891314	IS6-like element ISRle39A family transposase	-

Region 2: 181231..197179

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
RLV_RS37905 (RLV_2194)	179017..179769	-	753	WP_104891314	IS6-like element ISRle39A family transposase	-
RLV_RS37910 (RLV_2195)	179928..180650	-	723	WP_104891278	response regulator	-
RLV_RS38435	180770..180970	+	201	WP_131618399	hypothetical protein	-
RLV_RS37915 (RLV_2197)	181231..182232	-	1002	WP_104891277	P-type DNA transfer ATPase VirB11	virB11
RLV_RS37920 (RLV_2198)	182229..183404	-	1176	WP_104891313	TrbI/VirB10 family protein	virB10
RLV_RS37925 (RLV_2199)	183604..184386	-	783	WP_077988073	TrbG/VirB9 family P-type conjugative transfer protein	virB9
RLV_RS37930 (RLV_2200)	184414..185088	-	675	WP_077988072	type IV secretion system protein	virB8
RLV_RS37935 (RLV_2201)	185181..186449	-	1269	WP_104891304	IS256 family transposase	-
RLV_RS37940 (RLV_2202)	186552..186710	+	159	Protein_190	IS6 family transposase	-
RLV_RS37945 (RLV_2203)	187042..187980	+	939	WP_245461634	lytic transglycosylase domain-containing protein	-
RLV_RS37950 (RLV_2204)	187999..188310	+	312	WP_077988068	TrbC/VirB2 family protein	virB2
RLV_RS37955	188394..188672	+	279	WP_104891276	VirB3 family type IV secretion system protein	virB3
RLV_RS37960 (RLV_2205)	188644..191025	+	2382	WP_077988070	DUF87 domain-containing protein	virb4
RLV_RS37965	191156..191959	+	804	WP_245315068	type IV secretion system protein	-
RLV_RS37970 (RLV_2207)	192000..193109	+	1110	WP_245315069	type IV secretion system protein	virB6
RLV_RS37975 (RLV_2208)	193322..193996	+	675	WP_077988072	type IV secretion system protein	virB8
RLV_RS37980 (RLV_2209)	194024..194806	+	783	WP_077988073	TrbG/VirB9 family P-type conjugative transfer protein	virB9
RLV_RS37985 (RLV_2210)	195006..196181	+	1176	WP_104891313	TrbI/VirB10 family protein	virB10
RLV_RS37990 (RLV_2211)	196178..197179	+	1002	WP_104891277	P-type DNA transfer ATPase VirB11	virB11
RLV_RS38440	197440..197640	-	201	WP_131618399	hypothetical protein	-
RLV_RS37995 (RLV_2212)	197760..198482	+	723	WP_104891278	response regulator	-
RLV_RS39465	198565..198654	+	90	Protein_203	IS6 family transposase	-
RLV_RS38000 (RLV_2214)	198716..199021	-	306	Protein_204	DDE-type integrase/transposase/recombinase	-
RLV_RS38005 (RLV_2215)	199127..200293	+	1167	WP_281060848	IS256 family transposase	-
RLV_RS38010 (RLV_2216)	200329..201012	+	684	Protein_206	IS5 family transposase	-

Host bacterium

• ID: 8012
• GenBank: NZ_CP025510
• Plasmid name: pRlvD
• Incompatibility group: -
• Plasmid size: 217776 bp
• Coordinate of oriT [Strand]: 120599..120632 [-]
• Host baterium: Rhizobium leguminosarum bv. viciae strain UPM791

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -