Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   112362
Name   oriT_pPlaYM7902C in_silico
Organism   Pseudomonas amygdali pv. lachrymans strain YM7902
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP127048 (39235..39414 [+], 180 nt)
oriT length   180 nt
IRs (inverted repeats)      80..87, 91..98  (CAAAGGGG..CCCCTTTG)
 42..47, 56..61  (AAAAAG..CTTTTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 180 nt

>oriT_pPlaYM7902C
ATCTCGAATTCGCTAAACAGGCACGTTACCGATTGTCTACAAAAAAGAGCTTCGCCTTTTTCGTAGCCAATCGACGTGCCAAAGGGGATACCCCTTTGAAACCCCGCAGAGCGGGAAAGCGTTGTCGTTGTCGTTGTTGGTTGTCGTCATTCAGGTGCCCTCAGGAGGTGATGTTGTGGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7995 GenBank   WP_052764764
Name   Relaxase_QO021_RS31250_pPlaYM7902C insolico UniProt ID   _
Length   416 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 416 a.a.        Molecular weight: 47026.70 Da        Isoelectric Point: 5.5334

>WP_052764764.1 relaxase/mobilization nuclease domain-containing protein [Pseudomonas amygdali]
MLIRVSGYNTGAQEYLEKGNKSGREFTRDELDHRLIIEGQLSLTRAIYESIPDYGQDRYLTFTLSFKEDT
VSPELLKSITTDFKNFFMHAYKPEEFNLYAEAHLPKMKTVTDRKTGEVIDRKPHIHIIIPRINLLSGNEA
NPVDVYRNHEKYFEAFQEHINQKYGLSSPRENVRADITDAASVLSRYKGDDFYGKNRQFKQDLVKQVIER
GVTTRADFYALVAEHGETRIRNQGKDTEYISVKLPGDAKGTNLKDTIFQDDFIVRRELKKPPLEASVSAQ
ATPPRSKVIEGTLIEHGEAPYQHKDTNQLSYFVTLKPEGGKPRTVWGVGLEEAMTDANLKQGDQVRLEDL
GTWPVVVQVIAEDGTTSDKTVNRRAWSAQPVAPEREVAETTPKGQAIAAGTPELSSPDEEDGMSMD

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(40-253)


  Protein structure



No available structure.




T4CP

ID   9196 GenBank   WP_005746152
Name   t4cp2_QO021_RS31205_pPlaYM7902C insolico UniProt ID   _
Length   557 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 557 a.a.        Molecular weight: 61711.38 Da        Isoelectric Point: 6.4342

>WP_005746152.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Pseudomonas syringae group]
MARAKSKPISPDNPQERIEEHPAILIGKHPTKDTFLASYGQTFVMLAAPPGTGKTVGVVTPNLLSYPDSV
VVNDPKFENWRDTAGFRAAAGHKVYRFSPELLETHRWNPLSALSRDPLYRLGQIRTLAGVLFVSDNPKNQ
EWYNKAANVFAAILLYLMEMEGMKLNGMKLTLPQAYEVASLGTGLGVWAQQAIEQHSNGPNALSVETLRE
LNGVFEASKNKSSGWSTTVDILRGALSMYAEKTVAWAVSDTDIDFTKLRKEKISIYFCVTGNAIKKYGPL
MNLFFTQAIQQNTDVMPEQGGHCADGTLILKYQVLFVIDEIAVMGRIEIMEMAPALTRGAGLRYIIIFQG
KDQLRSERTYGREAGNGIMQAFHIEIVYGTGNVELAKEYSTRLGNTTVRVHNQSLNRQKHEIGARGQTDS
YSEQPRPLLLPQEVSALPYGEELIFVEATKTTPAANIRARKIFWYEEPVFKERAGMPTPDVPIGDASKID
ALTVPVRTVEAKVAVADTKPMQAEQRQRWNPKDKASEVAQAEAVKAQPVDVEPDPEPAQADDTLDTM

  Protein domains


Predicted by InterproScan.

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

(26-477)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 17518..27872

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QO021_RS31085 (QO021_31080) 13230..13511 - 282 WP_002556029 type II toxin-antitoxin system RelE/ParE family toxin -
QO021_RS31090 (QO021_31085) 13511..13699 - 189 WP_002556028 hypothetical protein -
QO021_RS31095 (QO021_31090) 13888..14523 - 636 WP_054068142 recombinase family protein -
QO021_RS31100 (QO021_31095) 14838..15470 + 633 WP_003381804 ParA family protein -
QO021_RS31105 (QO021_31100) 15506..15760 + 255 WP_003381801 hypothetical protein -
QO021_RS31110 (QO021_31105) 16185..16850 - 666 WP_004667059 LexA family transcriptional regulator -
QO021_RS31115 (QO021_31110) 16938..17168 + 231 WP_032704469 Cro/CI family transcriptional regulator -
QO021_RS31120 (QO021_31115) 17518..18207 + 690 WP_005746161 lytic transglycosylase domain-containing protein virB1
QO021_RS31125 (QO021_31120) 18204..18542 + 339 WP_017279422 hypothetical protein -
QO021_RS31130 (QO021_31125) 18555..19031 + 477 WP_080544547 VirB3 family type IV secretion system protein virB3
QO021_RS31135 (QO021_31130) 18970..21444 + 2475 WP_054068314 VirB4 family type IV secretion system protein virb4
QO021_RS31140 (QO021_31135) 21441..22127 + 687 WP_004667979 P-type DNA transfer protein VirB5 -
QO021_RS31145 (QO021_31140) 22160..22525 + 366 WP_004643103 hypothetical protein -
QO021_RS31150 (QO021_31145) 22536..23468 + 933 WP_004667984 type IV secretion system protein virB6
QO021_RS31155 (QO021_31150) 23542..23808 + 267 WP_005746157 hypothetical protein -
QO021_RS31160 (QO021_31155) 23845..24633 + 789 WP_004667986 virB8 family protein virB8
QO021_RS31165 (QO021_31160) 24623..25432 + 810 WP_004667987 P-type conjugative transfer protein VirB9 virB9
QO021_RS31170 (QO021_31165) 25419..26807 + 1389 WP_004667989 TrbI/VirB10 family protein virB10
QO021_RS31175 (QO021_31170) 26817..27872 + 1056 WP_005746155 P-type DNA transfer ATPase VirB11 virB11
QO021_RS31180 (QO021_31175) 27886..28272 + 387 WP_005746154 hypothetical protein -
QO021_RS31185 (QO021_31180) 28257..28622 + 366 WP_004667995 hypothetical protein -
QO021_RS31190 (QO021_31185) 28669..28935 + 267 WP_004644125 hypothetical protein -
QO021_RS31195 (QO021_31190) 29060..31471 + 2412 WP_044299713 ATP-binding protein -
QO021_RS31200 (QO021_31195) 31587..31820 + 234 WP_004666680 hypothetical protein -

Host bacterium

ID   12797 GenBank   NZ_CP127048
Plasmid name   pPlaYM7902C Incompatibility group   -
Plasmid size   53818 bp Coordinate of oriT [Strand]   39235..39414 [+]
Host baterium   Pseudomonas amygdali pv. lachrymans strain YM7902

Cargo genes

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