Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 121206
• Name: oriT_pXF-P4.OLS0478
• Organism: Xylella fastidiosa strain OLS0478
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CM003753 (9859..9964 [-], 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-P4.OLS0478
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTGCCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_ADT32_RS00310_pXF-P4.OLS0478

• ID: 13391
• GenBank: WP_060871446
• Name: traI_ADT32_RS00310_pXF-P4.OLS0478
• UniProt ID: _
• Length: 830 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 830 a.a.
• Molecular weight: 92949.91 Da
• Isoelectric Point: 10.6024

>WP_060871446.1 TraI/MobA(P) family conjugative relaxase [Xylella fastidiosa]
MIAKHVPMRVVRKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVLDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESRVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKRYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQAQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKEKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTNRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVRKANTDYLKARDAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQVRRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFEDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQSQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSYELMAVDKYIAERELKRVRMFDIMKHRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTNKGTLKTKGRNR

Protein domains

Predicted by InterproScan.

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

• Relaxase/Mobilisation nuclease domain (Relaxase) (13-250)

Protein structure

No available structure.

T4CP

t4cp2_ADT32_RS00315_pXF-P4.OLS0478

• ID: 15691
• GenBank: WP_060871447
• Name: t4cp2_ADT32_RS00315_pXF-P4.OLS0478
• UniProt ID: _
• Length: 644 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 644 a.a.
• Molecular weight: 72027.53 Da
• Isoelectric Point: 8.4086

>WP_060871447.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNEEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNHNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGTNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDTL
RLVHEPTLLDEIKI

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (430-627)

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (121-417)

Protein structure

No available structure.

t4cp2_ADT32_RS00460_pXF-P4.OLS0478

• ID: 15692
• GenBank: WP_060871461
• Name: t4cp2_ADT32_RS00460_pXF-P4.OLS0478
• UniProt ID: _
• Length: 854 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 854 a.a.
• Molecular weight: 95613.66 Da
• Isoelectric Point: 6.3106

>WP_060871461.1 conjugal transfer protein TrbE [Xylella fastidiosa]
MFQIITIAIALVGAVLLIWLFLLVQRANADLRLKNHRSKDAGVADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASLDNAWMVHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESMGTLYEGVFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLINHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHVDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEHSARQLEKAINALAFTARVETVNTMDAYVG
SLPGHGVENVRRPLLNTMNLADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSESKSSTLSEFLVTVQDTVIREALKPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLAHTT
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNNR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIAMIRKLEALHGDAWVHEWLCLKGLR
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: 31699..40513

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
ADT32_RS00385 (ADT32_00160)	27300..27614	+	315	WP_060871452	TrfB-related DNA-binding protein	-
ADT32_RS00390 (ADT32_00165)	27694..27948	+	255	WP_060871453	hypothetical protein	-
ADT32_RS00395 (ADT32_00170)	27945..28307	+	363	WP_060871454	PIN domain-containing protein	-
ADT32_RS00400 (ADT32_00175)	28378..28605	-	228	WP_057683524	hypothetical protein	-
ADT32_RS00405 (ADT32_00180)	28602..28970	-	369	WP_060871455	hypothetical protein	-
ADT32_RS13400	29738..30988	-	1251	WP_155641466	hypothetical protein	-
ADT32_RS00420 (ADT32_00195)	31088..31693	-	606	WP_040123201	conjugal transfer protein TrbN	-
ADT32_RS00425 (ADT32_00200)	31699..33069	-	1371	WP_060871457	P-type conjugative transfer protein TrbL	virB6
ADT32_RS00430 (ADT32_00205)	33091..33327	-	237	WP_057683527	EexN family lipoprotein	-
ADT32_RS00435 (ADT32_00210)	33344..34117	-	774	WP_060871458	P-type conjugative transfer protein TrbJ	virB5
ADT32_RS00440 (ADT32_00215)	34136..35536	-	1401	WP_060871459	TrbI/VirB10 family protein	virB10
ADT32_RS00445 (ADT32_00220)	35542..36018	-	477	WP_057683530	conjugal transfer protein TrbH	-
ADT32_RS00450 (ADT32_00225)	36021..36911	-	891	WP_057683531	P-type conjugative transfer protein TrbG	virB9
ADT32_RS00455 (ADT32_00230)	36928..37644	-	717	WP_060871460	conjugal transfer protein TrbF	virB8
ADT32_RS00460 (ADT32_00235)	37641..40205	-	2565	WP_060871461	conjugal transfer protein TrbE	virb4
ADT32_RS00465 (ADT32_00240)	40193..40513	-	321	WP_060871462	conjugal transfer protein TrbD	virB3

Host bacterium

• ID: 21634
• GenBank: NZ_CM003753
• Plasmid name: pXF-P4.OLS0478
• Incompatibility group: -
• Plasmid size: 40515 bp
• Coordinate of oriT [Strand]: 9859..9964 [-]
• Host baterium: Xylella fastidiosa strain OLS0478

Cargo genes

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