Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100170
Name   oriT_pXF51 in_silico
Organism   Xylella fastidiosa 9a5c
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_002490 (39539..39580 [+], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      6..11, 12..17  (GGTTTT..AAAACC)
Location of nic site      24..25
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   

  oriT sequence  


Download         Length: 42 nt

>oriT_pXF51
ATAGCGGTTTTAAAACCTATCCTGCCCTAGATTTAACCCTCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   163 GenBank   WP_052262879
Name   VirD2_pXF51 insolico UniProt ID   _
Length   458 a.a. PDB ID   
Note   Type IV secretory pathway, VirD2 components (relaxase)

  Relaxase protein sequence


Download         Length: 458 a.a.        Molecular weight: 52136.31 Da        Isoelectric Point: 10.8138

>WP_052262879.1 relaxase/mobilization nuclease domain-containing protein [Xylella fastidiosa]
MGIIEAELGSALSPAVKRKVNNTKKLRSTAKRVTGRSSEVMVKVTGFGKGAGHVKAHLDYITRNGKLEME
NDRGEIFNGKEEVKEFFKDWEKDFGDGKRHKNQRDTMHMVLSMPETTDSESVKKSVREFAKATFGKNHEY
VFVLHTDEPHPHCHLTVKCLGFDGIRLNPRKADLHQWREGFAEKLRDQGVEAEATPRRSRGVVKKAEPNV
IRHIERGDKTHEPRVSKVKAAKVKEAAMELVAESKGLPVPPKPWEEAIKARQREIRRAWLTVAAELEREN
TRKTFNQKEARNDRPNYERISAEQARPAQRAASVYQSNLTKAGRQAPSRTVSSLRNVSCLGVVQHRSSSK
MLLQPNAPDRMGRNGRPNSEMRRSGTSNNGVDRDAKMLLDVYKPIEQNKVLAWRIRSFVEAMPSIETERH
QIKRDLAQRFTKQAEKIHRKTNGQEQTGPKRGGKDVER

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(53-203)


  Protein structure



No available structure.




T4CP

ID   163 GenBank   WP_010895213
Name   VirD4_pXF51 insolico UniProt ID   Q9PHI9
Length   656 a.a. PDB ID   _
Note   The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion.

  T4CP protein sequence


Download         Length: 656 a.a.        Molecular weight: 72836.33 Da        Isoelectric Point: 8.6439

>WP_010895213.1 type IV secretory system conjugative DNA transfer family protein [Xylella fastidiosa]
MVIIALVAVVTGVWAYLAGGIFLMAFGHKFEESTPLTLYQYWFYYGAEKQAKKWLYISSGISLAVLLAPL
LFFFSHAEKSLFGDARFAKLREIKNAGLMGKRGIILGLYMNTYLLFGGSQHVSISAPTRSGKGVGIVIPN
LLSWPDSVVCSDIKIENFAITSAYRQKHGQECYLFNPVSTEYKTHRYNPLSYISEDPHFRIDDIQKIGNM
LFPDVPGTDVIWTATPRSLFLGIVLMLLETQGKLVTFGQVLRETLQDGDGSVYFGKIINERAKAGNPYSG
PCIRALNSYISIASENTRSGVMTSFRSKLELWMNPIIDAATSGNDFDLRDLRKKRMSVFVGVTPDNLKRL
APLLNLFYQQLIDLNTRELPEHNPALKYQCLLMMDEFTALGKLDCLADGISFIAGYGLRLLPIFQSPAQI
VGKYGEAAAETFSTNHAAQIIYPPKVTEIKTAREISEWLGFQTVKGVSESKGKGIFTKKSESQSISDQRR
ALLLPQEITSLGSKRALVVVEDCPPILAKRIRYFREHVFMDRLKSVSPSLAKFGNKLPNEKQLKAIIESG
ELAVKVPVIDIDEHICMVSGSTVAQTTVVVQSNGKTEVHVFERLITPADMPNLAKIALANLNIDFSAVEK
AKDGQLDEAALHSYVENLSKQSLDNV

  Protein domains


Predicted by InterproScan.

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

(88-540)

  Protein structure


Source ID Structure
AlphaFold DB Q9PHI9


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 435..13189

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
XF_RS12140 (XF_a0001) 47..301 + 255 WP_042464021 helix-turn-helix transcriptional regulator -
XF_RS12145 (XF_a0002) 435..1010 + 576 WP_010895199 lytic transglycosylase domain-containing protein virB1
XF_RS12150 (XF_a0003) 1012..2994 + 1983 WP_010895200 type I DNA topoisomerase -
XF_RS12155 (XF_a0004) 3065..3328 + 264 WP_010895201 hypothetical protein -
XF_RS12160 (XF_a0005) 3353..3709 + 357 WP_069106970 TrbC/VirB2 family protein virB2
XF_RS12165 (XF_a0006) 3712..4080 + 369 WP_010895203 type IV secretion system protein VirB3 virB3
XF_RS12170 (XF_a0007) 4094..6541 + 2448 WP_010895204 VirB4 family type IV secretion system protein virb4
XF_RS12175 (XF_a0008) 6538..7218 + 681 WP_010895205 P-type DNA transfer protein VirB5 virB5
XF_RS12185 (XF_a0010) 7542..7790 + 249 WP_010895207 hypothetical protein -
XF_RS12190 (XF_a0011) 7794..8840 + 1047 WP_010895208 type IV secretion system protein virB6
XF_RS12195 (XF_a0012) 9150..9971 + 822 WP_010895209 virB8 family protein virB8
XF_RS12200 (XF_a0013) 9982..10818 + 837 WP_010895210 P-type conjugative transfer protein VirB9 virB9
XF_RS12205 (XF_a0014) 10818..12161 + 1344 WP_010895211 type IV secretion system protein VirB10 virB10
XF_RS12210 (XF_a0015) 12158..13189 + 1032 WP_042464027 P-type DNA transfer ATPase VirB11 virB11
XF_RS12215 (XF_a0016) 13155..15164 + 2010 WP_042464030 type IV secretory system conjugative DNA transfer family protein -
XF_RS12220 (XF_a0017) 15175..17466 + 2292 WP_010895214 LPD7 domain-containing protein -
XF_RS12225 17463..17660 + 198 WP_042464033 hypothetical protein -
XF_RS12230 (XF_a0018) 17657..17983 + 327 WP_010895215 hypothetical protein -

Host bacterium

ID   163 GenBank   NC_002490
Plasmid name   pXF51 Incompatibility group   PromA-like
Plasmid size   51158 bp Coordinate of oriT [Strand]   39539..39580 [+]
Host baterium   Xylella fastidiosa 9a5c

Cargo genes

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