Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105811
Name   oriT_pXFAS_5235 in_silico
Organism   Xylella fastidiosa subsp. fastidiosa strain IVIA5235
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP047172 (32992..33097 [-], 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_5235
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTACCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3922 GenBank   WP_004086668
Name   Relaxase_D1605_RS11410_pXFAS_5235 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   3935 GenBank   WP_004086690
Name   t4cp2_D1605_RS11310_pXFAS_5235 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   3936 GenBank   WP_004086666
Name   t4cp2_D1605_RS11415_pXFAS_5235 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: 12804..22985

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
D1605_RS11240 (D1605_011380) 7812..8405 - 594 WP_004086728 LPD29 domain-containing protein -
D1605_RS11245 (D1605_011385) 8582..8896 - 315 WP_012382835 TrfB-related DNA-binding protein -
D1605_RS11250 (D1605_011390) 8964..9557 - 594 WP_004086726 LPD29 domain-containing protein -
D1605_RS11255 (D1605_011395) 9888..10451 - 564 WP_004086710 recombinase family protein -
D1605_RS11260 (D1605_011400) 10994..11362 + 369 WP_004086708 hypothetical protein -
D1605_RS11265 (D1605_011405) 11359..11586 + 228 WP_004086706 hypothetical protein -
D1605_RS11270 (D1605_011410) 12199..12798 - 600 WP_004086719 conjugal transfer protein TrbN -
D1605_RS11275 (D1605_011415) 12804..14174 - 1371 WP_004086703 P-type conjugative transfer protein TrbL virB6
D1605_RS11280 (D1605_011420) 14196..14432 - 237 WP_012382834 EexN family lipoprotein -
D1605_RS11285 (D1605_011425) 14449..15222 - 774 WP_004086702 P-type conjugative transfer protein TrbJ virB5
D1605_RS11290 (D1605_011430) 15241..16641 - 1401 WP_012382833 TrbI/VirB10 family protein virB10
D1605_RS11295 (D1605_011435) 16647..17123 - 477 WP_004086697 conjugal transfer protein TrbH -
D1605_RS11300 (D1605_011440) 17126..18016 - 891 WP_004086695 P-type conjugative transfer protein TrbG virB9
D1605_RS11305 (D1605_011445) 18033..18749 - 717 WP_004086692 conjugal transfer protein TrbF virB8
D1605_RS11310 (D1605_011450) 18746..21310 - 2565 WP_004086690 conjugal transfer protein TrbE virb4
D1605_RS11315 (D1605_011455) 21298..21618 - 321 WP_004086725 conjugal transfer protein TrbD virB3
D1605_RS11320 (D1605_011460) 21621..22013 - 393 WP_004086717 TrbC/VirB2 family protein virB2
D1605_RS11325 (D1605_011465) 22026..22985 - 960 WP_038231439 P-type conjugative transfer ATPase TrbB virB11
D1605_RS11330 (D1605_011470) 23192..23548 - 357 WP_012382841 transcriptional regulator -
D1605_RS11335 (D1605_011475) 23666..24025 + 360 WP_012382840 single-stranded DNA-binding protein -
D1605_RS11340 (D1605_011480) 24069..24425 + 357 WP_004086687 hypothetical protein -
D1605_RS11345 (D1605_011485) 24447..25358 + 912 WP_004086685 replication protein RepA -
D1605_RS11350 (D1605_011490) 26081..26401 + 321 WP_012382839 KleE stable inheritance protein -
D1605_RS11355 (D1605_011495) 26442..27638 - 1197 WP_004086683 RNA-guided endonuclease TnpB family protein -
D1605_RS11360 (D1605_011500) 27632..27886 - 255 Protein_29 recombinase family protein -

Host bacterium

ID   6248 GenBank   NZ_CP047172
Plasmid name   pXFAS_5235 Incompatibility group   -
Plasmid size   38297 bp Coordinate of oriT [Strand]   32992..33097 [-]
Host baterium   Xylella fastidiosa subsp. fastidiosa strain IVIA5235

Cargo genes

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