Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114822
Name   oriT_pXFAS_R2XF4358-18 in_silico
Organism   Xylella fastidiosa subsp. fastidiosa strain R2XF4358/18
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP109899 (38101..38206 [+], 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  


Download         Length: 106 nt

>oriT_pXFAS_R2XF4358-18
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTACCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9504 GenBank   WP_004086668
Name   traI_OK115_RS11725_pXFAS_R2XF4358-18 insolico UniProt ID   B2IAU3
Length   830 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 830 a.a.        Molecular weight: 92664.59 Da        Isoelectric Point: 10.5711

>WP_004086668.1 TraI/MobA(P) family conjugative relaxase [Xylella fastidiosa]
MIAKHVPMRVVKKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVLDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESRVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKSYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQVQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKAKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTKRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVEKANTDYLKARDAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQARRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFDDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQAQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSSELMAVDKYIAERELKRVREFDIMKNRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTKKGTLKTKGRNR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)

Large polyvalent protein-associated domain 7 (LPD7)

(463-550)


  Protein structure


Source ID Structure
AlphaFold DB B2IAU3


T4CP

ID   11068 GenBank   WP_004086690
Name   t4cp2_OK115_RS11620_pXFAS_R2XF4358-18 insolico UniProt ID   _
Length   854 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 854 a.a.        Molecular weight: 95956.03 Da        Isoelectric Point: 6.3394

>WP_004086690.1 conjugal transfer protein TrbE [Xylella fastidiosa]
MFQIITIAIALLGTVLLIWLFLLVQRANADLRLKNHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASFDNAWMVHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESIDTLYEGFFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLIDHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHVDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEQSARRLEKAINALAFTARVETINTMDAYLG
SLPGHGVENVRRPLLNTMNFADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSKSKASTLSEFIVTVQDEVIREALKPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLSHTT
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.



ID   11069 GenBank   WP_004086666
Name   t4cp2_OK115_RS11720_pXFAS_R2XF4358-18 insolico UniProt ID   _
Length   644 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 644 a.a.        Molecular weight: 72064.60 Da        Isoelectric Point: 8.5739

>WP_004086666.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNDEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNRNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKGRLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGFNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDTL
RLVHEPTLLDEIKI

  Protein domains


Predicted by InterproScan.

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

(429-627)

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

(119-417)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 9916..20097

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OK115_RS11570 (OK115_11570) 5015..5269 + 255 Protein_8 recombinase family protein -
OK115_RS11575 (OK115_11575) 5263..6459 + 1197 WP_004086683 RNA-guided endonuclease TnpB family protein -
OK115_RS11580 (OK115_11580) 6500..6820 - 321 WP_012382839 KleE stable inheritance protein -
OK115_RS11585 (OK115_11585) 7543..8454 - 912 WP_004086685 replication protein RepA -
OK115_RS11590 (OK115_11590) 8476..8832 - 357 WP_004086687 hypothetical protein -
OK115_RS11595 (OK115_11595) 8876..9235 - 360 WP_012382840 single-stranded DNA-binding protein -
OK115_RS11600 (OK115_11600) 9353..9709 + 357 WP_012382841 transcriptional regulator -
OK115_RS11605 (OK115_11605) 9916..10875 + 960 WP_038231439 P-type conjugative transfer ATPase TrbB virB11
OK115_RS11610 (OK115_11610) 10888..11280 + 393 WP_004086717 TrbC/VirB2 family protein virB2
OK115_RS11615 (OK115_11615) 11283..11603 + 321 WP_004086725 conjugal transfer protein TrbD virB3
OK115_RS11620 (OK115_11620) 11591..14155 + 2565 WP_004086690 conjugal transfer protein TrbE virb4
OK115_RS11625 (OK115_11625) 14152..14868 + 717 WP_004086692 conjugal transfer protein TrbF virB8
OK115_RS11630 (OK115_11630) 14885..15775 + 891 WP_004086695 P-type conjugative transfer protein TrbG virB9
OK115_RS11635 (OK115_11635) 15778..16254 + 477 WP_004086697 conjugal transfer protein TrbH -
OK115_RS11640 (OK115_11640) 16260..17660 + 1401 WP_012382833 TrbI/VirB10 family protein virB10
OK115_RS11645 (OK115_11645) 17679..18452 + 774 WP_004086702 P-type conjugative transfer protein TrbJ virB5
OK115_RS11650 (OK115_11650) 18469..18705 + 237 WP_012382834 EexN family lipoprotein -
OK115_RS11655 (OK115_11655) 18727..20097 + 1371 WP_004086703 P-type conjugative transfer protein TrbL virB6
OK115_RS11660 (OK115_11660) 20103..20702 + 600 WP_004086719 conjugal transfer protein TrbN -
OK115_RS11665 (OK115_11665) 21315..21542 - 228 WP_004086706 hypothetical protein -
OK115_RS11670 (OK115_11670) 21539..21907 - 369 WP_004086708 hypothetical protein -
OK115_RS11675 (OK115_11675) 22450..23013 + 564 WP_004086710 recombinase family protein -
OK115_RS11680 (OK115_11680) 23344..23937 + 594 WP_004086726 LPD29 domain-containing protein -
OK115_RS11685 (OK115_11685) 24005..24319 + 315 WP_012382835 TrfB-related DNA-binding protein -
OK115_RS11690 (OK115_11690) 24496..25089 + 594 WP_004086728 LPD29 domain-containing protein -

Host bacterium

ID   15257 GenBank   NZ_CP109899
Plasmid name   pXFAS_R2XF4358-18 Incompatibility group   -
Plasmid size   38297 bp Coordinate of oriT [Strand]   38101..38206 [+]
Host baterium   Xylella fastidiosa subsp. fastidiosa strain R2XF4358/18

Cargo genes

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