Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116275
Name   oriT_pXF-CFBP8478 in_silico
Organism   Xylella fastidiosa strain CFBP8478
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP135135 (30448..30553 [+], 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-CFBP8478
GCTAGCCTCGCAGAGCAGGATTCCCGTTGAGTGCCGAAGGTGCGAATAAGGGAAAGTGAAGAAGGAACACCGGATTTCCGGTGGGCCTACTTCACATATCCTGCCC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10410 GenBank   WP_057683541
Name   traI_RO838_RS11990_pXF-CFBP8478 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: 92979.06 Da        Isoelectric Point: 10.6169

>WP_057683541.1 TraI/MobA(P) family conjugative relaxase [Xylella fastidiosa]
MIAKHVPMRVVKKSDFRELVKYLSNQQGKQERVGCVTVTNCFQNNVMDAALEVQATQALNTRSEADKTYH
LLISFREGENPAPEILEVIESRVCAALGYADYQRVSVVHHDTDNLHIHVAINKIHPKRYTIHTPYNDYKT
LGEICKKLEREYGLEADNHTVRKTVGENRADDMERNAGVESLLGWIKRECTDQIKQAQSWSELHAVMQRN
GLEIRERGNGLVITNGVGRSVKASSVARDFSKEKLEARFGAFESFVKQAPSVSSVHARRIQAPLVEKVGR
RPPPRSKGRTPSLSSVGVLHVNSGIRYEQRPIYVKQASTAELYAMYKLEQQDLGAVRNVAIARARTNRDR
KIEATKRLGRIKRAAIKLMRGPGVNKKLLYALARKSLKEGVRKANTDYLKVRNAAYATYHRRVWADWLQV
QATQGNAEALAALRAREMRQWWSCNIFGGLQVRRTGPVPGLKPDNITKAGTIIYRVGSTAIRDDGDLLNV
SHGAGDYGVEAALRMAMYRYGERITVKGSDEFKKRVVQIAAAARLNISFEDEVLDKRRKQLVSDAAVIVK
LTDAMLSDKTAQFTQVQASRVGAFQEDALSEYDAAISRSINLANQEQINEQQRTRAKHYFVQRWSDRGGP
NSRRDGHATRIRSGGGGSGKHGASGATVISSAGGFNKPNVGGIGAKPPPASTHRLRNLHQLGVVQFSRGS
EVLLPRHVSDCVGEQQTERNHRVRRDVHTAGITSYELMAVDKYIAERELKRVRMFDIMKHRRYNEDDAGM
VKFAGLRQVDGKSLVLLKRNDEVIVLAIDVATARRMKRFSLGDEVLLTNKGTLKTKGRNR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-250)

Large polyvalent protein-associated domain 7 (LPD7)

(463-550)


  Protein structure



No available structure.




T4CP

ID   12150 GenBank   WP_057683542
Name   t4cp2_RO838_RS11985_pXF-CFBP8478 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: 72013.50 Da        Isoelectric Point: 8.4086

>WP_057683542.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MRKPNNAVGPQVRGGQRKKNKLVPALALTSMATGLQVATQYFAHTFNYQSTLGGNYNHIYAPWSILSWYA
KWGDQFHNYFFAAGNIGMMVTAGGLIGTALIKTFEINSVKANEYLHGSACWASKKDIEQSGLLGNDEGVY
VGAWEDKDGRLHYLRHNGPEHVLTYAPTRSGKGVGLVVPTLLSWPHSVVVTDLKGELWAMTAGWRQKHAK
NKVIRFEPATLNGSVCWNPLDEIRIGTEYEVGDVQNLATLIVDPNGKGLESHWQKTSQALLVGVILHVLY
KRKNEGFPATLSYVDHIMSDPNHNVAELWMEMTQYGHINGENHPAVGSAGRDMMDRPEEEAGSVLSTAKS
YIALYRDPVVARNVSKSDFCIKDLMNHDDPVSLYIVTQPNDKARLRPLVRVMLNMIVRLLADKMKFERVP
TELSWWRQILTKLGTNQVADFHVRSKKSYKHRLLGMIDEFPSLGKLEIMQESLAFVAGYGIKFYLICQDL
NQLKSRETGYGPDETITSNCHVQNAYPPNRVETAEHLSKLTGQTTVLKEQITTSGKRATPILGQLSRTIQ
EVQRPLLTVDECLRMPGPKKDAEGQITEAGDMVVYVAGYPAIYGKQPLYFQDPIFIARAAVPEPKTSDTL
RLVHEPTLLDEIKI

  Protein domains


Predicted by InterproScan.

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

(431-627)

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

(119-417)

  Protein structure



No available structure.



ID   12151 GenBank   WP_057683532
Name   t4cp2_RO838_RS12080_pXF-CFBP8478 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: 95824.81 Da        Isoelectric Point: 6.0995

>WP_057683532.1 conjugal transfer protein TrbE [Xylella fastidiosa]
MFQIITIAIALLGAVLLIWLFLLVQRANADLRLKNHRSKDAGVADLLNYAAVVDDGVIVGKNGSFMASWL
YRGADNASATEAERELISFRINQALASLDNAWMIHVDAVRRPAPSYSDPSLSHFPDAVSAAVDEERRRLF
ESIDTLYEGFFVVTVTWFPPVLAERRFVELMFHDDAEKPNDKTRTAHLIDHFKREVINLENRLSLAVELE
RLRGVKITKEDGSTVTHDQQLQWLHFCVTGLNHPIQLPSNPMYIDSLIGGQELYPGVVPKIGRNFIQVVA
IEGFPLESYPGILSVLAELPIEYRWSSRFIFLDHHEAVSHLEKFRKKWKQKMRGFFDQVFNTNTSHVDED
AVSMVADASSAIAETNSGLVSQGYYTSVVVLMNESREQVEHSARRLEKAINALAFTARVETVNTMDAYLG
SLPGHGVENVRRPLLNTMNLADLLPTSTIWTGENRAPSPLFPPNAPPLLHGVTSGNSPMRINLHVRDLGH
CIIFGPTRTGKSTKLALVAFQWRRYLGARIYAFDKGLSMYPTCKAMHGHHFSIASNTDKLAFAPLSRLDT
RTRRAWAMEWIDTILALNGVITSPAQRNAIAEAILSMSESKASTLSEFLVTVQDEVIREALEPYTVDGNM
GYLLDAVEDGLELADFMTFEIEQLMGLGEKFALPVLLYLFMRIEESLSEEDARPTLLILDEAWLMLSHAT
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: 39053..47589

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RO838_RS12030 (RO838_12030) 34375..35139 - 765 WP_004091486 ParA family protein -
RO838_RS12035 (RO838_12035) 35142..35441 - 300 WP_057683547 transcriptional regulator KorA -
RO838_RS12040 (RO838_12040) 35637..35957 - 321 WP_057683534 KleE stable inheritance protein -
RO838_RS12045 (RO838_12045) 36676..37587 - 912 WP_004091489 replication protein RepA -
RO838_RS12050 (RO838_12050) 37631..37978 - 348 WP_050812600 hypothetical protein -
RO838_RS12055 (RO838_12055) 38022..38381 - 360 WP_004091494 single-stranded DNA-binding protein -
RO838_RS12060 (RO838_12060) 38499..38855 + 357 WP_012382841 transcriptional regulator -
RO838_RS12065 (RO838_12065) 39053..40012 + 960 WP_046417547 P-type conjugative transfer ATPase TrbB virB11
RO838_RS12070 (RO838_12070) 40025..40417 + 393 WP_046417535 TrbC/VirB2 family protein virB2
RO838_RS12075 (RO838_12075) 40420..40740 + 321 WP_057683533 conjugal transfer protein TrbD virB3
RO838_RS12080 (RO838_12080) 40728..43292 + 2565 WP_057683532 conjugal transfer protein TrbE virb4
RO838_RS12085 (RO838_12085) 43289..44005 + 717 WP_046417528 conjugal transfer protein TrbF virB8
RO838_RS12090 (RO838_12090) 44022..44912 + 891 WP_057683531 P-type conjugative transfer protein TrbG virB9
RO838_RS12095 (RO838_12095) 44915..45391 + 477 WP_057683530 conjugal transfer protein TrbH -
RO838_RS12100 (RO838_12100) 45397..46797 + 1401 WP_057683529 TrbI/VirB10 family protein virB10
RO838_RS12105 (RO838_12105) 46816..47589 + 774 WP_057683528 P-type conjugative transfer protein TrbJ virB5
RO838_RS12110 (RO838_12110) 47606..47842 + 237 WP_057683527 EexN family lipoprotein -

Host bacterium

ID   16708 GenBank   NZ_CP135135
Plasmid name   pXF-CFBP8478 Incompatibility group   -
Plasmid size   47863 bp Coordinate of oriT [Strand]   30448..30553 [+]
Host baterium   Xylella fastidiosa strain CFBP8478

Cargo genes

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