Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102442
Name   oriT_pXFAS01-Dixon in_silico
Organism   Xylella fastidiosa subsp. multiplex strain Dixon
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JARTVJ010000009 (26821..26926 [+], 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_pXFAS01-Dixon
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTACCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1826 GenBank   WP_004086668
Name   Relaxase_P9196_RS12615_pXFAS01-Dixon 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   1414 GenBank   WP_004086690
Name   t4cp2_P9196_RS12510_pXFAS01-Dixon 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   1415 GenBank   WP_004086666
Name   t4cp2_P9196_RS12610_pXFAS01-Dixon 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: 3..8817

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
P9196_RS12505 (P9196_12510) 3..323 + 321 WP_004086725 conjugal transfer protein TrbD virB3
P9196_RS12510 (P9196_12515) 311..2875 + 2565 WP_004086690 conjugal transfer protein TrbE virb4
P9196_RS12515 (P9196_12520) 2872..3588 + 717 WP_004086692 conjugal transfer protein TrbF virB8
P9196_RS12520 (P9196_12525) 3605..4495 + 891 WP_004086695 P-type conjugative transfer protein TrbG virB9
P9196_RS12525 (P9196_12530) 4498..4974 + 477 WP_004086697 conjugal transfer protein TrbH -
P9196_RS12530 (P9196_12535) 4980..6380 + 1401 WP_012382833 TrbI/VirB10 family protein virB10
P9196_RS12535 (P9196_12540) 6399..7172 + 774 WP_004086702 P-type conjugative transfer protein TrbJ virB5
P9196_RS12540 (P9196_12545) 7189..7425 + 237 WP_012382834 EexN family lipoprotein -
P9196_RS12545 (P9196_12550) 7447..8817 + 1371 WP_004086703 P-type conjugative transfer protein TrbL virB6
P9196_RS12550 (P9196_12555) 8823..9422 + 600 WP_004086719 conjugal transfer protein TrbN -
P9196_RS12555 (P9196_12560) 10035..10262 - 228 WP_004086706 hypothetical protein -
P9196_RS12560 (P9196_12565) 10259..10627 - 369 WP_004086708 hypothetical protein -
P9196_RS12565 (P9196_12570) 11170..11733 + 564 WP_004086710 recombinase family protein -
P9196_RS12570 (P9196_12575) 12064..12657 + 594 WP_004086726 LPD29 domain-containing protein -
P9196_RS12575 (P9196_12580) 12725..13039 + 315 WP_012382835 TrfB-related DNA-binding protein -
P9196_RS12580 (P9196_12585) 13216..13809 + 594 WP_004086728 LPD29 domain-containing protein -

Host bacterium

ID   2886 GenBank   NZ_JARTVJ010000009
Plasmid name   pXFAS01-Dixon Incompatibility group   -
Plasmid size   38298 bp Coordinate of oriT [Strand]   26821..26926 [+]
Host baterium   Xylella fastidiosa subsp. multiplex strain Dixon

Cargo genes

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