Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 121742
• Name: oriT_pAt4
• Organism: Agrobacterium tumefaciens strain cl001
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP048579 (24070..24126 [-], 57 nt)
• oriT length: 57 nt
• IRs (inverted repeats): 24..30, 35..41 (ACGTCGC..GCGACGT)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 57 nt

>oriT_pAt4
CCCCGCCAGGGGGCAAAAGCAGAACGTCGCGTCAGCGACGTATAATTGCGCCCTTGG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traA_FY131_RS28980_pAt4

• ID: 13722
• GenBank: WP_174007848
• Name: traA_FY131_RS28980_pAt4
• UniProt ID: _
• Length: 1107 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1107 a.a.
• Molecular weight: 122852.83 Da
• Isoelectric Point: 9.9028

>WP_174007848.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium tumefaciens]
MAVPHFSVSIVARGSGRSAVLSAAYRHCARMEYEREARTIDYTRKQGLLHEEFVIPADAPNWLRAMIADR
SVSGASEAFWNKVEVFEKRVDAQLAKDVTIALPIELSSEQNIALMRDFVAEHITSKGMVADWVYHDAPGN
PHVHLMTTLRPLSGDGFGAKKVAVLGPDGQPMRNDTGKIIYELWGGGTEDFNAFRDGWFAVQNRHLALAG
LDIRIDGRSFEKQGIDLTPTIHIGVGATAIERKSETENGPATARSRKLERIELQEERRAENVRRIQRNPG
IVLDLITREKSVFDNQDVAKILHRYVDDAALFQSLMARIMQHLDVLRLDRERIDFTSGVRTPARYTTREM
IRLEAEMANRSIWLSQRSSHGVRQKIIEAVFELHERLSDEQKTAIERVAGPERIAAVIGRAGAGKTTMMK
AAREAWEAAGYRVVGAALAGKAAEGLEKEAGILSRTLSSWELRWAQGRDHLDDKTVLVLDEAGMVSSKQM
AQLVEEATVRGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQHEQWMRDASLDLARGNIAKA
VASYSTNGRMMGSTLKSQAVENLISDWNREYDPARSSLILAHLRRDVRMLNELARAKLVERGLVDDGHAF
KTEDGIRHFAAGDQIVFLKNEGSLGVKNGMLAKVVEATPGRIVAEIGEGEHRKAISVEQRFYNNVDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHRDDLGVYYGSRSFAKGGGLAELLSRKNSKETTLDYE
KGAFYRAALRFADARGLHLVNVARTLVRDRLDWTVRQKQKLVNLTARLATIGAQLGLKRSNTQVTPKPVM
EARPMVSGITTFPKSIDQAVEDRLAADPGLKKQWQEVTTRFTQVFAEPETAFKAVNVDAMLKDPARAQTT
LAKIAAEPERFGALKGKTGIFTGANEKAARDTALVNAPALARNLERYVTARAEAERKHEAQERAIRLKVS
VDIPALSPSARQTLERIRDAIDRNDLPAGLEYALADRNVKAELEGFAKAVSERFGERSLLPISAKDANGE
TFHKLTAGMSPSQKNEVQSAWNNMRTVQQLAAHERTTLALKQAETARQTQTKGLSLK

Protein domains

Predicted by InterproScan.

• Viral (Superfamily 1) RNA helicase (Viral_helicase1) (697-740)

• AAA domain (AAA_30) (387-570)

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

• BID domain of Bartonella effector protein (Bep) (Bep_C_terminal) (863-958)

Protein structure

No available structure.

T4CP

traG_FY131_RS28965_pAt4

• ID: 16037
• GenBank: WP_174007844
• Name: traG_FY131_RS28965_pAt4
• UniProt ID: _
• Length: 645 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 645 a.a.
• Molecular weight: 69773.06 Da
• Isoelectric Point: 9.1773

>WP_174007844.1 Ti-type conjugative transfer system protein TraG [Agrobacterium tumefaciens]
MTATRILLAVVPPLMMIAIAFALPGIEQWLATFGKTAEAKLQLGRIGLALPYVASAAIALIVLFGTQGSV
NIKTAGWGSVAGSVAVIALAIVREGIRLSQFAGELPAVRSILSYIDPATMTGATAALFSGIFALRVAVIG
NAAFSRSEPKRIRGKRALHGEAEWMKLPEAGKLFAEDGGIVIGERYRVDRDSTAALSFRADMPETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVKAHRIKAGRDVIVLD
PKDPDIGFNALDWIGQHGGTKEEDIAAVASWIMSESGRASGVRDDFFRASGLQLLTAIIADVCLSGHTEK
KDQTLRTVRMNLSEPEPKLRARLQEIYDNSESDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYPNYA
GLVSGSTFSTDDIASGTTDVFVALDLKTLETHGGLARVIIGSFLNAIYNRDGAMPGRALFLLDEVARLGF
MRILETARDAGRKYGITLLMIYQSIGQMRETYGGRDATSKWFESASWISFSAINDPETADYISRRCGTTT
VEIDQVSRSFQARGSSRTRSKQLASRPLIQPHEVLRMRADEQIVFTGGNAPLRCGRAMWFRRADMKSCVG
DNRFHGKRGPLEIKV

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (164-637)

Protein structure

No available structure.

t4cp2_FY131_RS29070_pAt4

• ID: 16038
• GenBank: WP_174007960
• Name: t4cp2_FY131_RS29070_pAt4
• UniProt ID: _
• Length: 811 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 811 a.a.
• Molecular weight: 91180.67 Da
• Isoelectric Point: 5.9860

>WP_174007960.1 conjugal transfer protein TrbE [Agrobacterium tumefaciens]
MVALRSLRPSAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESATDFERNDLSRQINTILSRLG
SGWMIQVEAVRIPTNDYPSAERSHFPDAVTRMIDDERRKHFEQERGHFESRHALVLTYRPPERRRSGVTR
YIYSDTESRTATYADTVLDSFRRSVREIEQYLGNVISIERMRTREVPERGGTRIARYDELFQFIRFCITG
ENHPVRLPEIPMYLDWLATAELEHGLTPKVENRFLSVIAIDGLPAESWPGILNSLDLLPLTYRWSSRFIF
LDAEEAKQRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMAMVAETEDAIAEASSQLVAYGYYTPVIIL
FDESREKLADKAESVRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINTRNLADLIPLNSVWS
GSPLAPCPFYPPDAPPLTQVASGSSPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYKGAQVFA
FDKGNSILPLTLAVDGNHYDIGGDTGEGARLAFCPLSDLSTDTDRAWASEWIETLVSLQGVTVTPDHRNA
ISRQIGLIAGAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDSLTLGQFQCFEIEQLMNMGE
RNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAERS
GIIDVLKESCPTKICLPNGAARESGTREFYERIGFNPRQIEIVAAAIPKREYYVTSPDGRRLFDMALGPL
TLSFVGASGKADLARIRELLSTYGKDWPTQWLNERGINRYA

Protein domains

Predicted by InterproScan.

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (193-400)

• ABC transporter (ABC_tran) (449-626)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29241..44581

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
FY131_RS28985 (FY131_28765)	27501..28067	+	567	WP_236761240	conjugative transfer signal peptidase TraF	-
FY131_RS28990 (FY131_28770)	28057..29223	+	1167	WP_174007850	conjugal transfer protein TraB	-
FY131_RS28995 (FY131_28775)	29241..29852	+	612	WP_174007852	TraH family protein	virB1
FY131_RS29000 (FY131_28780)	29885..30505	-	621	WP_174007854	RES family NAD+ phosphorylase	-
FY131_RS29005 (FY131_28785)	30506..31261	-	756	WP_236761239	XRE family transcriptional regulator	-
FY131_RS29010 (FY131_28790)	31395..31646	-	252	WP_174007856	hypothetical protein	-
FY131_RS29015 (FY131_28795)	31950..32654	+	705	WP_174007858	transcriptional regulator TraR	-
FY131_RS29020 (FY131_28800)	32669..32968	-	300	WP_174007861	transcriptional repressor TraM	-
FY131_RS29025 (FY131_28805)	33520..34239	+	720	WP_174007863	LuxR family transcriptional regulator	-
FY131_RS29030 (FY131_28810)	34357..35019	+	663	WP_174007864	acyl-homoserine-lactone synthase	-
FY131_RS29035 (FY131_28815)	35059..36354	-	1296	WP_174007867	IncP-type conjugal transfer protein TrbI	virB10
FY131_RS29040 (FY131_28820)	36367..36810	-	444	WP_174007869	conjugal transfer protein TrbH	-
FY131_RS29045 (FY131_28825)	36814..37644	-	831	WP_174007871	P-type conjugative transfer protein TrbG	virB9
FY131_RS29050 (FY131_28830)	37660..38322	-	663	WP_174007873	conjugal transfer protein TrbF	virB8
FY131_RS29055 (FY131_28835)	38344..39525	-	1182	WP_174007875	P-type conjugative transfer protein TrbL	virB6
FY131_RS29060 (FY131_28840)	39530..39706	-	177	WP_142174475	entry exclusion protein TrbK	-
FY131_RS29065 (FY131_28845)	39700..40503	-	804	WP_174007877	P-type conjugative transfer protein TrbJ	virB5
FY131_RS29070 (FY131_28850)	40496..42931	-	2436	WP_174007960	conjugal transfer protein TrbE	virb4
FY131_RS29075 (FY131_28855)	42942..43241	-	300	WP_015647762	conjugal transfer protein TrbD	virB3
FY131_RS29080 (FY131_28860)	43234..43626	-	393	WP_174007879	TrbC/VirB2 family protein	virB2
FY131_RS29085 (FY131_28865)	43616..44581	-	966	WP_174007881	P-type conjugative transfer ATPase TrbB	virB11

Host bacterium

• ID: 22169
• GenBank: NZ_CP048579
• Plasmid name: pAt4
• Incompatibility group: -
• Plasmid size: 44881 bp
• Coordinate of oriT [Strand]: 24070..24126 [-]
• Host baterium: Agrobacterium tumefaciens strain cl001

Cargo genes

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