Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121207
Name   oriT_pXF-P4.OLS0479 in_silico
Organism   Xylella fastidiosa strain COF0407
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM003763 (16390..16495 [+], 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-P4.OLS0479
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTGCCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13392 GenBank   WP_046417493
Name   traI_ADT33_RS00295_pXF-P4.OLS0479 insolico UniProt ID   _
Length   830 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 830 a.a.        Molecular weight: 92904.89 Da        Isoelectric Point: 10.5707

>WP_046417493.1 TraI/MobA(P) family conjugative relaxase [Xylella fastidiosa]
MIAKHVPMRVVKKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVMDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESHVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKRYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQAQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKEKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTNRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVRKANTDYLKARDAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQVRRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFEDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQAQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSYELMAVDKYIAERELKRVRMFDIMKHRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTNKGTLKTKGRNR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(463-550)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)


  Protein structure



No available structure.




T4CP

ID   15693 GenBank   WP_046417494
Name   t4cp2_ADT33_RS00290_pXF-P4.OLS0479 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: 72074.59 Da        Isoelectric Point: 8.5743

>WP_046417494.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNDEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNHNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGTNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDKL
RFVHEPTLLDEIKI

  Protein domains


Predicted by InterproScan.

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

(431-629)

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

(119-417)

  Protein structure



No available structure.



ID   15694 GenBank   WP_046417530
Name   t4cp2_ADT33_RS00385_pXF-P4.OLS0479 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: 95693.78 Da        Isoelectric Point: 6.3113

>WP_046417530.1 conjugal transfer protein TrbE [Xylella fastidiosa]
MFQIITIAIALLGAVLLIWLFLLVQRANADLRLKNHRSKDAGLADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASLDNAWMVHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESMGTLYEGVFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLIDHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHIDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEHSARQLEKAINALAFTARVETINTMDAYVG
SLPGHGVENVRRPLLNTMNLADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSESKSSTLSEFIVTVQDAVIREALKPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLAHTT
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNNR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIAMIRKLEALHGDAWVHEWLRLKGLR
LDEYVSPNDYGVAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(620-778)

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: 24762..35040

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ADT33_RS00335 (ADT33_11555) 20306..21070 - 765 WP_046417477 ParA family protein -
ADT33_RS00340 (ADT33_11560) 21067..21372 - 306 WP_046417543 transcriptional regulator KorA -
ADT33_RS13220 (ADT33_11565) 21568..21888 - 321 WP_046417474 KleE stable inheritance protein -
ADT33_RS00350 (ADT33_11570) 22385..23296 - 912 WP_004091489 replication protein RepA -
ADT33_RS00355 (ADT33_11575) 23340..23687 - 348 WP_050812600 hypothetical protein -
ADT33_RS00360 (ADT33_11580) 23731..24090 - 360 WP_004091494 single-stranded DNA-binding protein -
ADT33_RS00365 (ADT33_11585) 24208..24564 + 357 WP_012382841 transcriptional regulator -
ADT33_RS00370 (ADT33_11590) 24762..25721 + 960 WP_046417547 P-type conjugative transfer ATPase TrbB virB11
ADT33_RS00375 (ADT33_11595) 25734..26126 + 393 WP_046417535 TrbC/VirB2 family protein virB2
ADT33_RS00380 (ADT33_11600) 26129..26449 + 321 WP_046417532 conjugal transfer protein TrbD virB3
ADT33_RS00385 (ADT33_11605) 26437..29001 + 2565 WP_046417530 conjugal transfer protein TrbE virb4
ADT33_RS00390 (ADT33_11610) 28998..29714 + 717 WP_046417528 conjugal transfer protein TrbF virB8
ADT33_RS00395 (ADT33_11615) 29731..30621 + 891 WP_046417527 P-type conjugative transfer protein TrbG virB9
ADT33_RS00400 (ADT33_11620) 30624..31100 + 477 WP_046417523 conjugal transfer protein TrbH -
ADT33_RS00405 (ADT33_11625) 31106..32506 + 1401 WP_046417521 TrbI/VirB10 family protein virB10
ADT33_RS00410 (ADT33_11630) 32525..33310 + 786 WP_046417519 P-type conjugative transfer protein TrbJ virB5
ADT33_RS00415 (ADT33_11635) 33323..33637 + 315 WP_155561293 EexN family lipoprotein -
ADT33_RS00420 (ADT33_11640) 33643..35040 + 1398 WP_046417516 P-type conjugative transfer protein TrbL virB6

Host bacterium

ID   21635 GenBank   NZ_CM003763
Plasmid name   pXF-P4.OLS0479 Incompatibility group   -
Plasmid size   35678 bp Coordinate of oriT [Strand]   16390..16495 [+]
Host baterium   Xylella fastidiosa strain COF0407

Cargo genes

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