Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114821
Name   oriT_pXFAS_5770 in_silico
Organism   Xylella fastidiosa subsp. fastidiosa strain IVIA5770
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP109893 (11242..11347 [-], 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_5770
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTACCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9503 GenBank   WP_004086668
Name   traI_OK114_RS11505_pXFAS_5770 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   11066 GenBank   WP_004086666
Name   t4cp2_OK114_RS11510_pXFAS_5770 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.



ID   11067 GenBank   WP_004086690
Name   t4cp2_OK114_RS11610_pXFAS_5770 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29351..38165

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OK114_RS11540 (OK114_11540) 24359..24952 - 594 WP_004086728 LPD29 domain-containing protein -
OK114_RS11545 (OK114_11545) 25129..25443 - 315 WP_012382835 TrfB-related DNA-binding protein -
OK114_RS11550 (OK114_11550) 25511..26104 - 594 WP_004086726 LPD29 domain-containing protein -
OK114_RS11555 (OK114_11555) 26435..26998 - 564 WP_004086710 recombinase family protein -
OK114_RS11560 (OK114_11560) 27541..27909 + 369 WP_004086708 hypothetical protein -
OK114_RS11565 (OK114_11565) 27906..28133 + 228 WP_004086706 hypothetical protein -
OK114_RS11570 (OK114_11570) 28746..29345 - 600 WP_004086719 conjugal transfer protein TrbN -
OK114_RS11575 (OK114_11575) 29351..30721 - 1371 WP_004086703 P-type conjugative transfer protein TrbL virB6
OK114_RS11580 (OK114_11580) 30743..30979 - 237 WP_012382834 EexN family lipoprotein -
OK114_RS11585 (OK114_11585) 30996..31769 - 774 WP_004086702 P-type conjugative transfer protein TrbJ virB5
OK114_RS11590 (OK114_11590) 31788..33188 - 1401 WP_012382833 TrbI/VirB10 family protein virB10
OK114_RS11595 (OK114_11595) 33194..33670 - 477 WP_004086697 conjugal transfer protein TrbH -
OK114_RS11600 (OK114_11600) 33673..34563 - 891 WP_004086695 P-type conjugative transfer protein TrbG virB9
OK114_RS11605 (OK114_11605) 34580..35296 - 717 WP_004086692 conjugal transfer protein TrbF virB8
OK114_RS11610 (OK114_11610) 35293..37857 - 2565 WP_004086690 conjugal transfer protein TrbE virb4
OK114_RS11615 (OK114_11615) 37845..38165 - 321 WP_004086725 conjugal transfer protein TrbD virB3
OK114_RS11620 (OK114_11620) 38168..38297 - 130 Protein_41 conjugal transfer protein -

Host bacterium

ID   15256 GenBank   NZ_CP109893
Plasmid name   pXFAS_5770 Incompatibility group   -
Plasmid size   38297 bp Coordinate of oriT [Strand]   11242..11347 [-]
Host baterium   Xylella fastidiosa subsp. fastidiosa strain IVIA5770

Cargo genes

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