Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120080
Name   oriT_pXF-Riv5 in_silico
Organism   Xylella fastidiosa subsp. multiplex strain Riv5
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP064327 (26822..26927 [+], 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_pXF-Riv5
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTACCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12648 GenBank   WP_004086668
Name   traI_IUD19_RS11080_pXF-Riv5 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   14847 GenBank   WP_004086690
Name   t4cp2_IUD19_RS10975_pXF-Riv5 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   14848 GenBank   WP_004086666
Name   t4cp2_IUD19_RS11075_pXF-Riv5 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
IUD19_RS10970 (IUD19_10970) 3..323 + 321 WP_004086725 conjugal transfer protein TrbD virB3
IUD19_RS10975 (IUD19_10975) 311..2875 + 2565 WP_004086690 conjugal transfer protein TrbE virb4
IUD19_RS10980 (IUD19_10980) 2872..3588 + 717 WP_004086692 conjugal transfer protein TrbF virB8
IUD19_RS10985 (IUD19_10985) 3605..4495 + 891 WP_004086695 P-type conjugative transfer protein TrbG virB9
IUD19_RS10990 (IUD19_10990) 4498..4974 + 477 WP_004086697 conjugal transfer protein TrbH -
IUD19_RS10995 (IUD19_10995) 4980..6380 + 1401 WP_012382833 TrbI/VirB10 family protein virB10
IUD19_RS11000 (IUD19_11000) 6399..7172 + 774 WP_004086702 P-type conjugative transfer protein TrbJ virB5
IUD19_RS11005 (IUD19_11005) 7189..7425 + 237 WP_012382834 EexN family lipoprotein -
IUD19_RS11010 (IUD19_11010) 7447..8817 + 1371 WP_004086703 P-type conjugative transfer protein TrbL virB6
IUD19_RS11015 (IUD19_11015) 8823..9422 + 600 WP_004086719 conjugal transfer protein TrbN -
IUD19_RS11020 (IUD19_11020) 10035..10262 - 228 WP_004086706 hypothetical protein -
IUD19_RS11025 (IUD19_11025) 10259..10627 - 369 WP_004086708 hypothetical protein -
IUD19_RS11030 (IUD19_11030) 11170..11733 + 564 WP_004086710 recombinase family protein -
IUD19_RS11035 (IUD19_11035) 12064..12657 + 594 WP_004086726 LPD29 domain-containing protein -
IUD19_RS11040 (IUD19_11040) 12725..13039 + 315 WP_012382835 TrfB-related DNA-binding protein -
IUD19_RS11045 (IUD19_11045) 13216..13809 + 594 WP_004086728 LPD29 domain-containing protein -

Host bacterium

ID   20510 GenBank   NZ_CP064327
Plasmid name   pXF-Riv5 Incompatibility group   -
Plasmid size   38299 bp Coordinate of oriT [Strand]   26822..26927 [+]
Host baterium   Xylella fastidiosa subsp. multiplex strain Riv5

Cargo genes

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