Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 116274
• Name: oriT_pXF-CO33
• Organism: Xylella fastidiosa strain CO33
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP135133 (32915..33020 [+], 106 nt)
• oriT length: 106 nt
• IRs (inverted repeats): 68..74, 77..83 (CACCGGA..TCCGGTG)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 106 nt

>oriT_pXF-CO33
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTGCCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_RO839_RS11995_pXF-CO33

• ID: 10409
• GenBank: WP_057683541
• Name: traI_RO839_RS11995_pXF-CO33
• UniProt ID: _
• Length: 830 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 830 a.a.
• Molecular weight: 92979.06 Da
• Isoelectric Point: 10.6169

>WP_057683541.1 TraI/MobA(P) family conjugative relaxase [Xylella fastidiosa]
MIAKHVPMRVVKKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVMDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESRVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKRYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQAQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKEKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTNRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVRKANTDYLKVRNAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQVRRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFEDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQVQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSYELMAVDKYIAERELKRVRMFDIMKHRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTNKGTLKTKGRNR

Protein domains

Predicted by InterproScan.

• Relaxase/Mobilisation nuclease domain (Relaxase) (12-250)

• Large polyvalent protein-associated domain 7 (LPD7) (463-550)

Protein structure

No available structure.

T4CP

t4cp2_RO839_RS11990_pXF-CO33

• ID: 12148
• GenBank: WP_057683542
• Name: t4cp2_RO839_RS11990_pXF-CO33
• UniProt ID: _
• Length: 644 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 644 a.a.
• Molecular weight: 72013.50 Da
• Isoelectric Point: 8.4086

>WP_057683542.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNDEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNHNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGTNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDTL
RLVHEPTLLDEIKI

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (431-627)

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (119-417)

Protein structure

No available structure.

t4cp2_RO839_RS12085_pXF-CO33

• ID: 12149
• GenBank: WP_057683532
• Name: t4cp2_RO839_RS12085_pXF-CO33
• UniProt ID: _
• Length: 854 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 854 a.a.
• Molecular weight: 95824.81 Da
• Isoelectric Point: 6.0995

>WP_057683532.1 conjugal transfer protein TrbE [Xylella fastidiosa]
MFQIITIAIALLGAVLLIWLFLLVQRANADLRLKNHRSKDAGVADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASLDNAWMIHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESIDTLYEGFFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLIDHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHVDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEHSARRLEKAINALAFTARVETVNTMDAYLG
SLPGHGVENVRRPLLNTMNLADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSESKASTLSEFLVTVQDEVIREALEPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLSHAT
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNNR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIAMIRKLEALHGDAWVHEWLRLKGLR
LDEYVSPNDYGVAA

Protein domains

Predicted by InterproScan.

• TraG P-loop domain (P-loop_TraG) (619-778)

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (220-431)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 41520..47379

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
RO839_RS12035 (RO839_12035)	36842..37606	-	765	WP_004091486	ParA family protein	-
RO839_RS12040 (RO839_12040)	37609..37908	-	300	WP_057683547	transcriptional regulator KorA	-
RO839_RS12045 (RO839_12045)	38104..38424	-	321	WP_057683534	KleE stable inheritance protein	-
RO839_RS12050 (RO839_12050)	39143..40054	-	912	WP_004091489	replication protein RepA	-
RO839_RS12055 (RO839_12055)	40098..40445	-	348	WP_050812600	hypothetical protein	-
RO839_RS12060 (RO839_12060)	40489..40848	-	360	WP_004091494	single-stranded DNA-binding protein	-
RO839_RS12065 (RO839_12065)	40966..41322	+	357	WP_012382841	transcriptional regulator	-
RO839_RS12070 (RO839_12070)	41520..42479	+	960	WP_046417547	P-type conjugative transfer ATPase TrbB	virB11
RO839_RS12075 (RO839_12075)	42492..42884	+	393	WP_046417535	TrbC/VirB2 family protein	virB2
RO839_RS12080 (RO839_12080)	42887..43207	+	321	WP_057683533	conjugal transfer protein TrbD	virB3
RO839_RS12085 (RO839_12085)	43195..45759	+	2565	WP_057683532	conjugal transfer protein TrbE	virb4
RO839_RS12090 (RO839_12090)	45756..46472	+	717	WP_046417528	conjugal transfer protein TrbF	virB8
RO839_RS12095 (RO839_12095)	46489..47379	+	891	WP_057683531	P-type conjugative transfer protein TrbG	virB9
RO839_RS12100 (RO839_12100)	47382..47858	+	477	WP_057683530	conjugal transfer protein TrbH	-

Host bacterium

• ID: 16707
• GenBank: NZ_CP135133
• Plasmid name: pXF-CO33
• Incompatibility group: -
• Plasmid size: 47863 bp
• Coordinate of oriT [Strand]: 32915..33020 [+]
• Host baterium: Xylella fastidiosa strain CO33

Cargo genes

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