Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121208
Name   oriT_pXF-P4.COF0407 in_silico
Organism   Xylella fastidiosa strain OLS0479
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM003744 (11834..11939 [+], 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.COF0407
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTGCCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13393 GenBank   WP_060871446
Name   traI_ADT31_RS00205_pXF-P4.COF0407 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: 92949.91 Da        Isoelectric Point: 10.6024

>WP_060871446.1 TraI/MobA(P) family conjugative relaxase [Xylella fastidiosa]
MIAKHVPMRVVRKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVLDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESRVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKRYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQAQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKEKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTNRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVRKANTDYLKARDAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQVRRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFEDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQSQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSYELMAVDKYIAERELKRVRMFDIMKHRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTNKGTLKTKGRNR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(463-550)

Relaxase/Mobilisation nuclease domain (Relaxase)

(13-250)


  Protein structure



No available structure.




T4CP

ID   15695 GenBank   WP_060871447
Name   t4cp2_ADT31_RS00200_pXF-P4.COF0407 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: 72027.53 Da        Isoelectric Point: 8.4086

>WP_060871447.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNEEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNHNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGTNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDTL
RLVHEPTLLDEIKI

  Protein domains


Predicted by InterproScan.

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

(430-627)

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

(121-417)

  Protein structure



No available structure.



ID   15696 GenBank   WP_060871461
Name   t4cp2_ADT31_RS00295_pXF-P4.COF0407 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: 95613.66 Da        Isoelectric Point: 6.3106

>WP_060871461.1 conjugal transfer protein TrbE [Xylella fastidiosa]
MFQIITIAIALVGAVLLIWLFLLVQRANADLRLKNHRSKDAGVADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASLDNAWMVHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESMGTLYEGVFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLINHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHVDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEHSARQLEKAINALAFTARVETVNTMDAYVG
SLPGHGVENVRRPLLNTMNLADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSESKSSTLSEFLVTVQDTVIREALKPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLAHTT
FRDKIEEWLRSMAKKNCSVLMATQSISEAAKSGILDIITESTACRIFLANPNAREEKTAEIYGRLGLNNR
QIEIIASAVPKRDYYYVSEKGRRLYQLALGPLALAFVGSTDKESIAMIRKLEALHGDAWVHEWLCLKGLR
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: 20339..30520

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ADT31_RS00245 (ADT31_00070) 15755..16519 - 765 WP_004091486 ParA family protein -
ADT31_RS00250 (ADT31_00075) 16522..16821 - 300 WP_060871463 transcriptional regulator KorA -
ADT31_RS13280 (ADT31_00080) 17017..17337 - 321 WP_012382839 KleE stable inheritance protein -
ADT31_RS00260 (ADT31_00085) 17961..18872 - 912 WP_004091489 replication protein RepA -
ADT31_RS00265 (ADT31_00090) 18917..19264 - 348 WP_050812600 hypothetical protein -
ADT31_RS00270 (ADT31_00095) 19308..19667 - 360 WP_004091494 single-stranded DNA-binding protein -
ADT31_RS00275 (ADT31_00100) 19785..20141 + 357 WP_012382841 transcriptional regulator -
ADT31_RS00280 (ADT31_00105) 20339..21298 + 960 WP_046417547 P-type conjugative transfer ATPase TrbB virB11
ADT31_RS00285 (ADT31_00110) 21311..21703 + 393 WP_046417535 TrbC/VirB2 family protein virB2
ADT31_RS00290 (ADT31_00115) 21706..22026 + 321 WP_060871462 conjugal transfer protein TrbD virB3
ADT31_RS00295 (ADT31_00120) 22014..24578 + 2565 WP_060871461 conjugal transfer protein TrbE virb4
ADT31_RS00300 (ADT31_00125) 24575..25291 + 717 WP_060871460 conjugal transfer protein TrbF virB8
ADT31_RS00305 (ADT31_00130) 25308..26198 + 891 WP_057683531 P-type conjugative transfer protein TrbG virB9
ADT31_RS00310 (ADT31_00135) 26201..26677 + 477 WP_057683530 conjugal transfer protein TrbH -
ADT31_RS00315 (ADT31_00140) 26683..28083 + 1401 WP_060871459 TrbI/VirB10 family protein virB10
ADT31_RS00320 (ADT31_00145) 28102..28875 + 774 WP_060871458 P-type conjugative transfer protein TrbJ virB5
ADT31_RS00325 (ADT31_00150) 28892..29128 + 237 WP_057683527 EexN family lipoprotein -
ADT31_RS00330 (ADT31_00155) 29150..30520 + 1371 WP_060871457 P-type conjugative transfer protein TrbL virB6
ADT31_RS00335 (ADT31_00160) 30526..31131 + 606 WP_040123201 conjugal transfer protein TrbN -
ADT31_RS12895 31231..32481 + 1251 WP_155641466 hypothetical protein -

Host bacterium

ID   21636 GenBank   NZ_CM003744
Plasmid name   pXF-P4.COF0407 Incompatibility group   -
Plasmid size   33048 bp Coordinate of oriT [Strand]   11834..11939 [+]
Host baterium   Xylella fastidiosa strain OLS0479

Cargo genes

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