oriTDB

oriT

The information of the oriT region

oriTDB ID	100048
Name	oriT_pTi-SAKURA
Organism	Agrobacterium tumefaciens
Sequence Completeness	incomplete
*NCBI accession of oriT* (coordinates [strand])**	NC_002147 (_)
oriT length	16 nt
IRs (inverted repeats)	1..6, 11..16 (CGTCGC..GCGACG)
*Location of nic* site**	_
Conserved sequence flanking the nic site	_
Note	Ti plasmid

oriT sequence

Download Length: 16 nt

                        >oriT_pTi-SAKURA
CGTCGCTGGCGCGACG                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

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] Suzuki K et al. (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene. 242(1-2):331-6. [PMID:10721727]

Relaxase

TraA_pTi-SAKURA

ID	46	GenBank	NP_053349
Name	TraA_pTi-SAKURA	UniProt ID	Q9R6F0
Length	1194 a.a.	PDB ID
Note	Dtr system oriT relaxase; Provisional

Relaxase protein sequence

Download Length: 1194 a.a. Molecular weight: 133752.08 Da Isoelectric Point: 9.4620

          >NP_053349.1 hypothetical protein pTi-SAKURA_p111 (plasmid) [Agrobacterium tumefaciens]

MAIAHFSASIVSRGDGRSAVLSAAYRHCAKMDYEREARTIDYTRKVGLLHEEFLLPDHAPKWVRMLIADR

SVAGASEAFWNRVEAFEKRIDAQLAKDLTVALPLELTAEQNIALVRDFVEKHILSRGMVADWVYHDNPGN

PHIHLMTTLRPLTEDGFGAKKVAVIGEDGEPLRTKAGKIVYELWAGGTDDFNAFRYAWFERMNHHLALNG

INLRVDGRSYEKQGIDLVPTIHLGVGAKAIERKAEGEGRKAELERLELNEERREENARRIRENPKLVLDL

ITREKSVFDERDVAKILHRYIDDAGMFRNMMARIMQSGQVLRLERERISLATGKREPSKFTTHELIRLEA

TMARSAMWLDRRSSHGVGKVLLDATFARHDRLSQEQRTALAHIAGANRIAAVVGRAGAGKTTMMKAARET

WEAAGYRVVGAALAGKAAEGLEKEAGIIARTLSSWELRWQQERDRLDDRTVMVLDEAGMVSSRQMAMLVQ

AATEAGAKLVLVGDPDQLQPIEAGAAFRAITDRIGYAELGTIYRQREAWMRRASVDLAHRQVGSALAAYD

RANLIHSHWSKDEAIASLIEDWNRDYDPARSSLILAHRRLDVRALNELARERLVGRGFVGEGFAFRTEEG

ERRFDAGDRIVFLKNEGSLGVKNGMLAKVVEAAPGRFVAEIGEGEDGRQVTVDQHLYANVDHGYATTIHK

SQGATVDDVRVLASGTMDRHLTYVALTRHRDAARLYVGMNEFTNRGGVLVDHGEAPYENKPENHDSYFVT

LETGEGKQNTIWGVDLRRAMAEAAPQIGDRIGLDHKGSEMVRLPDGKKVKRHTWKVVDIRELALSRMTER

MSRDAAKETTLDYENASFYRAALRFADTHGLRVMNVARTMMRDRLDWTVRQKQRLARLGSRLLAIGGKLG

LVSSTHQQQSLSSNMKEVRPMVAGITIHPKSLDQAVEDKLAADPGLKKQWEEVSSRFHLIYAQPEAAFRA

VDVDAALKDPATAKSTLAKIANEPESFGALKGKTGLFASRVEKEDRDIAHVNAPALSRDLERYLQMRTNA

MQRLEAEERAIRHRVSIDIPALSPSARTVLERVRDAIDRNDLPAALGYAVSDKEAKLEIDGFNKAVSERF

GERSLLTNAAREPSGRLFEQLAKGLQPQEKEHLAEAWPVMRTAQQLAAHERTAATLKQVEDLRLSQRQTP

VIKQ

Protein domains

Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(686-735)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(949-1045)

AAA domain (AAA_30)

(382-568)

Protein structure

Source	ID	Structure
AlphaFold DB	Q9R6F0

Reference

[1] Suzuki K et al. (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene. 242(1-2):331-6. [PMID:10721727]

ID	76	GenBank	NP_053348
Name	TraC_pTi-SAKURA	UniProt ID	Q9R6F1
Length	98 a.a.	PDB ID	_
Note	conjugal transfer protein TraC; Provisional

Auxiliary protein sequence

Download Length: 98 a.a. Molecular weight: 10267.36 Da Isoelectric Point: 6.4153

                        >NP_053348.1 hypothetical protein pTi-SAKURA_p110 (plasmid) [Agrobacterium tumefaciens]

MKKPSSKIREEIARLQDQLRQAETREAERIGRVALKAGLGEIEIEEAELQAAFEDIAGRFRGGKAGTSGR

KNAGDGRTAGEPGATLASGSDAGSRGEA

Protein domains

Predicted by InterproScan.

TraC-like protein (TraC)

(2-97)

Protein structure

Source	ID	Structure
AlphaFold DB	Q9R6F1

Reference

[1] Suzuki K et al. (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene. 242(1-2):331-6. [PMID:10721727]

ID	77	GenBank	NP_053347
Name	TraD_pTi-SAKURA	UniProt ID	Q9R6F2
Length	71 a.a.	PDB ID	_
Note	conjugal transfer protein TraD; Provisional

Auxiliary protein sequence

Download Length: 71 a.a. Molecular weight: 7856.02 Da Isoelectric Point: 10.5480

                        >NP_053347.1 hypothetical protein pTi-SAKURA_p109 (plasmid) [Agrobacterium tumefaciens]

MHRTASTDARKKDTREKIELGGLIVKAGLRYEKRALLLGMLIDAGRRIKGDDAERSRLTTIGAEAFGRDG

E

Protein domains

Predicted by InterproScan.

Conjugal transfer protein TraD (TraD)

(8-67)

Protein structure

Source	ID	Structure
AlphaFold DB	Q9R6F2

Reference

[1] Suzuki K et al. (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene. 242(1-2):331-6. [PMID:10721727]

T4CP

TraG_pTi-SAKURA

ID	46	GenBank	NP_053346
Name	TraG_pTi-SAKURA	UniProt ID	Q9R6F3
Length	649 a.a.	PDB ID	_
Note	conjugal transfer coupling protein TraG

T4CP protein sequence

Download Length: 649 a.a. Molecular weight: 70083.12 Da Isoelectric Point: 9.3425

                        >NP_053346.1 hypothetical protein pTi-SAKURA_p108 (plasmid) [Agrobacterium tumefaciens]

MTANRILLAVVPATTMIAAVILMPGIEHWLAAFGRTAQAKLMLGRFGIALPYIAAAAIGTMFLFAANGAA

NIKTAGWGVVSGNVAAIIIAMIREAARLSGIAGSVPTDQSVLAYTDPATALGAAGPFLAGVFALRVVIKG

NAAFASPAPRRVRGKRAVHGEADWMGVVEAGRLFPDAGGIVIGERYRVDRDSVAGMSFRADQRETWGAGG

KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVSEHRRKAGRKVIVLD

PATPAIGFNALDWIGRFGGTKEEDIVAVATWIMTDNARTASARDDFFRASAMQLLTALIADVCLSGHTDE

QDQTLRRVRANLSEPEPKLRERLTRIYEQSESEFVRENVAVFVNMTPETFSGVYANAVKETHWLSYPNYA

ALVSGDSFSTDDLAKGETDIFIALDLKVLEAHPGLARVVIGAFLNAIYNRNGEVEGRTLFLLDEVARLGY

LRILETARDAGRKYGITLTLIFQSLGQMREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT

IEVDQTNRSTGMKGSSRSRSKQLSNRRLILPHEVMRMRTDEQIVFTAGNAPLRCGRAIWFRRDEMTRIVG

KNRFHQGDAPAKGPEPSTP

Protein domains

Predicted by InterproScan.

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

(164-635)

Protein structure

Source	ID	Structure
AlphaFold DB	Q9R6F3

Reference

[1] Suzuki K et al. (2000) Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene. 242(1-2):331-6. [PMID:10721727]

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 7308..16975

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HXC48_RS00015 (pTi-SAKURA_p003)	2594..3319	-	726	WP_003523894	nopaline ABC transporter permease NocM	-
HXC48_RS00020 (pTi-SAKURA_p004)	3321..4031	-	711	WP_010891638	nopaline ABC transporter permease NocQ	-
HXC48_RS00025 (pTi-SAKURA_p005)	4106..4957	-	852	WP_010891637	nopaline ABC transporter substrate-binding protein NocT	-
HXC48_RS00030 (pTi-SAKURA_p006)	5022..5795	-	774	WP_010891636	nopaline ABC transporter ATP-binding protein NocP	-
HXC48_RS00035 (pTi-SAKURA_p007)	6037..6951	+	915	WP_233278942	LysR family transcriptional regulator	-
HXC48_RS00040	7048..7257	-	210	WP_172690757	hypothetical protein	-
HXC48_RS00045 (pTi-SAKURA_p008)	7308..8624	-	1317	WP_010891634	IncP-type conjugal transfer protein TrbI	virB10
HXC48_RS00050 (pTi-SAKURA_p009)	8637..9113	-	477	WP_010891633	conjugal transfer protein TrbH	-
HXC48_RS00055 (pTi-SAKURA_p010)	9113..9967	-	855	WP_010891632	P-type conjugative transfer protein TrbG	virB9
HXC48_RS00060 (pTi-SAKURA_p011)	9985..10647	-	663	WP_010891631	conjugal transfer protein TrbF	virB8
HXC48_RS00065 (pTi-SAKURA_p012)	10662..11858	-	1197	WP_010974835	P-type conjugative transfer protein TrbL	virB6
HXC48_RS00070 (pTi-SAKURA_p013)	11852..12070	-	219	WP_010891629	entry exclusion protein TrbK	-
HXC48_RS00075 (pTi-SAKURA_p014)	12067..12825	-	759	WP_233278946	P-type conjugative transfer protein TrbJ	virB5
HXC48_RS00080 (pTi-SAKURA_p015)	12842..15310	-	2469	WP_010891627	conjugal transfer protein TrbE	virb4
HXC48_RS00085 (pTi-SAKURA_p016)	15321..15620	-	300	WP_010891626	conjugal transfer protein TrbD	virB3
HXC48_RS00090 (pTi-SAKURA_p017)	15613..16014	-	402	WP_010891625	conjugal transfer pilin TrbC	virB2
HXC48_RS00095 (pTi-SAKURA_p018)	16004..16975	-	972	WP_010891624	P-type conjugative transfer ATPase TrbB	virB11
HXC48_RS00100 (pTi-SAKURA_p019)	16972..17607	-	636	WP_010891623	acyl-homoserine-lactone synthase	-
HXC48_RS00105 (pTi-SAKURA_p020)	17971..19188	+	1218	WP_010891622	plasmid partitioning protein RepA	-
HXC48_RS00110 (pTi-SAKURA_p021)	19418..20428	+	1011	WP_010891621	plasmid partitioning protein RepB	-
HXC48_RS00115 (pTi-SAKURA_p023)	20643..21962	+	1320	WP_010891620	plasmid replication protein RepC	-

Region 2: 140576..150026

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HXC48_RS00680 (pTi-SAKURA_p141)	135962..136693	-	732	WP_010891505	(dimethylallyl)adenosine tRNA methylthiotransferase	-
HXC48_RS00685 (pTi-SAKURA_p142)	137530..140031	+	2502	WP_010891504	two-component system sensor kinase VirA	-
HXC48_RS00690 (pTi-SAKURA_p143)	140576..141313	+	738	WP_010891503	type IV secretion system lytic transglycosylase VirB1	virB1
HXC48_RS00695 (pTi-SAKURA_p144)	141313..141678	+	366	WP_010891502	pilin major subunit VirB2	virB2
HXC48_RS00700 (pTi-SAKURA_p145)	141678..142004	+	327	WP_010891501	type IV secretion system protein VirB3	virB3
HXC48_RS00705 (pTi-SAKURA_p146)	142004..144373	+	2370	WP_010891500	type IV secretion/conjugal transfer ATPase VirB4	virb4
HXC48_RS00710 (pTi-SAKURA_p147)	144390..145052	+	663	WP_010891499	pilin minor subunit VirB5	-
HXC48_RS00715 (pTi-SAKURA_p148)	145153..146040	+	888	WP_010891498	type IV secretion system protein	virB6
HXC48_RS00720 (pTi-SAKURA_p149)	146076..146243	+	168	WP_010891497	type IV secretion system lipoprotein VirB7	-
HXC48_RS00725 (pTi-SAKURA_p150)	146230..146943	+	714	WP_010891496	type IV secretion system protein VirB8	virB8
HXC48_RS00730 (pTi-SAKURA_p151)	146940..147821	+	882	WP_010891495	P-type conjugative transfer protein VirB9	virB9
HXC48_RS00735 (pTi-SAKURA_p152)	147818..148951	+	1134	WP_010891494	type IV secretion system protein VirB10	virB10
HXC48_RS00740 (pTi-SAKURA_p153)	148992..150026	+	1035	WP_010891493	P-type DNA transfer ATPase VirB11	virB11
HXC48_RS00745 (pTi-SAKURA_p154)	150245..151006	+	762	WP_010891492	two-component system response regulator VirG	-
HXC48_RS00750 (pTi-SAKURA_p155)	151148..151756	-	609	WP_010891491	conjugal transfer protein VirC2	-
HXC48_RS00755 (pTi-SAKURA_p156)	151759..152454	-	696	WP_010891490	conjugal transfer ATPase VirC1	-
HXC48_RS00760 (pTi-SAKURA_p157)	152725..153168	+	444	WP_010891489	T-DNA border endonuclease subunit VirD1	-
HXC48_RS00765 (pTi-SAKURA_p158)	153202..154545	+	1344	WP_010891488	T-DNA border endonuclease VirD2	-

Host bacterium

ID	46	GenBank	NC_002147
Plasmid name	pTi-SAKURA	Incompatibility group	_
Plasmid size	206479 bp	Coordinate of oriT [Strand]
Host baterium	Agrobacterium tumefaciens

Cargo genes

Drug resistance gene	-
Virulence gene	virulence-tumorigenic; virulence ( vir* ) gene regions for pathogenicity*
Metal resistance gene	-
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	-

Detailed information of oriT

oriT

The information of the oriT region

oriT sequence

oriT secondary structure

Reference

Relaxase

Relaxase protein sequence

Protein domains

Protein structure

Reference

Auxiliary protein

Auxiliary protein sequence

Protein domains

Protein structure

Reference

Auxiliary protein sequence

Protein domains

Protein structure

Reference

T4CP

T4CP protein sequence

Protein domains

Protein structure

Reference

T4SS

Host bacterium

Cargo genes