Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100655
Name   oriT_pXF51-J1 in_silico
Organism   Xylella fastidiosa strain J1a12
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NZ_CP009825 (39560..39601 [+], 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   predicted by the oriTfinder

  oriT sequence  


Download         Length: 42 nt

>oriT_pXF51-J1
ATAGCGGTTTTAAAACCTATCCTGCCCTAGATTTAACCCTCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   727 GenBank   WP_010895239
Name   Nickase_pXF51-J1 insolico UniProt ID   _
Length   463 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 463 a.a.        Molecular weight: 52664.98 Da        Isoelectric Point: 10.8467

>WP_010895239.1 relaxase/mobilization nuclease domain-containing protein [Xylella fastidiosa]
MAGRLMGIIEAELGSALSPAVKRKVNNTKKLRSTAKRVTGRSSEVMVKVTGFGKGAGHVKAHLDYITRNG
KLEMENDRGEIFNGKEEVKEFFKDWEKDFGDGKRHKNQRDTMHMVLSMPETTDSESVKKSVREFAKATFG
KNHEYVFVLHTDEPHPHCHLTVKCLGFDGIRLNPRKADLHQWREGFAEKLRDQGVEAEATPRRSRGVVKK
AEPNVIRHIERGDKTHEPRVSKVKAAKVKEAAMELVAESKGLPVPPKPWEEAIKARQREIRRAWLTVAAE
LERENTRKTFNQKEARNDRPNYERISAEQARPAQRAASVYQSNLTKAGRQAPSRTVSSLRNVSCLGVVQH
RSSSKMLLQPNAPDRMGRNGRPNSEMRRSGTSNNGVDRDAKMLLDVYKPIEQNKVLAWRIRSFVEAMPSI
ETERHQIKRDLAQRFTKQAEKIHRKTNGQEQTGPKRGGKDVER

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(58-208)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 435..13192

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OY18_RS13880 (OY18_13075) 47..301 + 255 WP_042464021 helix-turn-helix transcriptional regulator -
OY18_RS13885 (OY18_13080) 435..1010 + 576 WP_010895199 lytic transglycosylase domain-containing protein virB1
OY18_RS13890 (OY18_13085) 1012..2994 + 1983 WP_010895200 type I DNA topoisomerase -
OY18_RS14595 3065..3229 + 165 WP_157291841 hypothetical protein -
OY18_RS13895 (OY18_13090) 3354..3710 + 357 WP_069106970 TrbC/VirB2 family protein virB2
OY18_RS13900 (OY18_13095) 3713..4081 + 369 WP_010895203 type IV secretion system protein VirB3 virB3
OY18_RS13905 (OY18_13100) 4095..6542 + 2448 WP_010895204 VirB4 family type IV secretion system protein virb4
OY18_RS13910 (OY18_13105) 6539..7219 + 681 WP_010895205 P-type DNA transfer protein VirB5 virB5
OY18_RS13920 (OY18_13115) 7796..8842 + 1047 WP_010895208 type IV secretion system protein virB6
OY18_RS13930 (OY18_13120) 9152..9973 + 822 WP_010895209 virB8 family protein virB8
OY18_RS13935 (OY18_13125) 10141..10821 + 681 WP_229926375 TrbG/VirB9 family P-type conjugative transfer protein virB9
OY18_RS13940 (OY18_13130) 10821..12164 + 1344 WP_010895211 type IV secretion system protein VirB10 virB10
OY18_RS13945 (OY18_13135) 12161..13192 + 1032 WP_042464027 P-type DNA transfer ATPase VirB11 virB11
OY18_RS15450 13158..13859 + 702 WP_268233942 type IV secretory system conjugative DNA transfer family protein -
OY18_RS13950 (OY18_13140) 13817..15169 + 1353 WP_268233943 type IV secretory system conjugative DNA transfer family protein -
OY18_RS13955 (OY18_13145) 15180..17471 + 2292 WP_010895214 LPD7 domain-containing protein -
OY18_RS13960 (OY18_13150) 17468..17665 + 198 WP_042464033 hypothetical protein -
OY18_RS13965 (OY18_13155) 17662..17988 + 327 WP_010895215 hypothetical protein -

Host bacterium

ID   1115 GenBank   NZ_CP009825
Plasmid name   pXF51-J1 Incompatibility group   _
Plasmid size   51180 bp Coordinate of oriT [Strand]   39560..39601 [+]
Host baterium   Xylella fastidiosa strain J1a12

Cargo genes

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