Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115408
Name   oriT_pP6qnrS1 in_silico
Organism   Pseudomonas aeruginosa
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MH061383 (100538..100889 [+], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_pP6qnrS1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTAGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   5792 GenBank   WP_001151524
Name   WP_001151524_pP6qnrS1 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22

ID   5793 GenBank   WP_001309237
Name   WP_001309237_pP6qnrS1 insolico UniProt ID   A0A5W1N5T0
Length   131 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 131 a.a.        Molecular weight: 15183.38 Da        Isoelectric Point: 9.9240

>WP_001309237.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(70-117)

TraY domain (TraY)

(16-59)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W1N5T0


T4CP

ID   11495 GenBank   WP_000009350
Name   traD_HTS06_RS00035_pP6qnrS1 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81488.99 Da        Isoelectric Point: 5.0504

>WP_000009350.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWIKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCSEQLWSAFVLAAVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   11496 GenBank   WP_001064247
Name   traC_HTS06_RS00675_pP6qnrS1 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99187.86 Da        Isoelectric Point: 5.8486

>WP_001064247.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYVESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 35744..46069

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTS06_RS00155 31048..31590 + 543 WP_000587837 AAA family ATPase -
HTS06_RS00160 32072..32263 - 192 WP_000951934 hypothetical protein -
HTS06_RS00165 32287..32514 + 228 WP_000248278 hypothetical protein -
HTS06_RS00170 32565..33575 + 1011 Protein_33 DUF3883 domain-containing protein -
HTS06_RS00175 33570..34763 + 1194 Protein_34 Tn3 family transposase -
HTS06_RS00180 34888..35037 + 150 WP_309473705 DUF6710 family protein -
HTS06_RS00185 35211..35744 - 534 WP_000731968 phospholipase D family protein -
HTS06_RS00190 35744..36739 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTS06_RS00195 36781..37941 - 1161 WP_000101711 type IV secretion system protein VirB10 virB10
HTS06_RS00200 37941..38825 - 885 WP_000735067 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTS06_RS00205 38836..39534 - 699 WP_000646594 virB8 family protein virB8
HTS06_RS00210 39753..40793 - 1041 WP_000886022 type IV secretion system protein virB6
HTS06_RS00215 40809..41036 - 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
HTS06_RS00220 41044..41757 - 714 WP_000749362 type IV secretion system protein virB5
HTS06_RS00225 41775..44375 - 2601 WP_001200711 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTS06_RS00230 44375..44692 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTS06_RS00235 44742..45035 - 294 WP_000209137 TrbC/VirB2 family protein virB2
HTS06_RS00240 45045..45326 - 282 WP_000440698 transcriptional repressor KorA -
HTS06_RS00245 45335..46069 - 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
HTS06_RS00250 46112..46483 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTS06_RS00255 46499..46876 + 378 WP_000504251 hypothetical protein -
HTS06_RS00260 46839..47153 + 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
HTS06_RS00265 47267..47500 + 234 WP_001191790 hypothetical protein -
HTS06_RS00270 47556..48197 + 642 WP_001694850 restriction endonuclease -
HTS06_RS00275 48461..49165 - 705 WP_001067855 IS6-like element IS26 family transposase -
HTS06_RS00280 49374..49865 + 492 WP_000528930 HEPN family nuclease -
HTS06_RS00285 49877..50635 + 759 WP_000494510 hypothetical protein -

Region 2: 99967..117828

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTS06_RS00575 95931..96365 + 435 WP_000845895 conjugation system SOS inhibitor PsiB -
HTS06_RS00580 96362..97124 + 763 Protein_117 plasmid SOS inhibition protein A -
HTS06_RS00780 97303..97452 + 150 Protein_118 plasmid maintenance protein Mok -
HTS06_RS00585 97394..97519 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTS06_RS00785 97739..97969 + 231 WP_001426396 hypothetical protein -
HTS06_RS00790 97967..98140 - 174 Protein_121 hypothetical protein -
HTS06_RS00590 98210..98416 + 207 WP_000547939 hypothetical protein -
HTS06_RS00595 98441..98728 + 288 WP_000107535 hypothetical protein -
HTS06_RS00600 98849..99670 + 822 WP_001234471 DUF932 domain-containing protein -
HTS06_RS00605 99967..100569 - 603 WP_000243709 transglycosylase SLT domain-containing protein virB1
HTS06_RS00610 100890..101273 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HTS06_RS00615 101460..102149 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HTS06_RS00620 102248..102643 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HTS06_RS00625 102676..103041 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HTS06_RS00630 103056..103367 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTS06_RS00635 103389..103955 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HTS06_RS00640 103942..104670 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTS06_RS00645 104670..106097 + 1428 WP_000146692 F-type conjugal transfer pilus assembly protein TraB traB
HTS06_RS00650 106087..106677 + 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
HTS06_RS00655 106664..106861 + 198 WP_001324648 conjugal transfer protein TrbD -
HTS06_RS00660 106873..107124 + 252 WP_001038342 conjugal transfer protein TrbG -
HTS06_RS00665 107121..107636 + 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HTS06_RS00670 107771..107992 + 222 WP_001278689 conjugal transfer protein TraR -
HTS06_RS00675 108152..110779 + 2628 WP_001064247 type IV secretion system protein TraC virb4
HTS06_RS00680 110776..111162 + 387 WP_000097319 type-F conjugative transfer system protein TrbI -
HTS06_RS00685 111159..111791 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTS06_RS00690 111788..112780 + 993 WP_000830187 conjugal transfer pilus assembly protein TraU traU
HTS06_RS00695 112789..113427 + 639 WP_000777688 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTS06_RS00700 113424..115232 + 1809 WP_000821847 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTS06_RS00705 115259..115516 + 258 WP_000864318 conjugal transfer protein TrbE -
HTS06_RS00710 115509..116252 + 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
HTS06_RS00715 116268..116615 + 348 WP_001287913 conjugal transfer protein TrbA -
HTS06_RS00720 116617..116931 - 315 WP_000415567 hypothetical protein -
HTS06_RS00725 117012..117296 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HTS06_RS00730 117283..117828 + 546 WP_000059850 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTS06_RS00805 117818..117901 + 84 Protein_151 conjugal transfer protein TrbJ -

Host bacterium

ID   15841 GenBank   NZ_MH061383
Plasmid name   pP6qnrS1 Incompatibility group   IncR
Plasmid size   117945 bp Coordinate of oriT [Strand]   100538..100889 [+]
Host baterium   Pseudomonas aeruginosa

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib, aac(3)-IId, qnrS1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -