Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102882
Name   oriT_pPSUO2 in_silico
Organism   Escherichia coli strain PSUO2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP011916 (10419..10542 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 88..93, 105..110  (ATAAAT..ATTTAT)
 41..48, 61..68  (AAAAACAA..TTGTTTTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pPSUO2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTGAATCATTAGCTTATGTTATAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   870 GenBank   WP_001254385
Name   WP_001254385_pPSUO2 insolico UniProt ID   A0A1Q9L2K4
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 8975.08 Da        Isoelectric Point: 10.1422

>WP_001254385.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVAEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A1Q9L2K4

ID   871 GenBank   WP_000124979
Name   WP_000124979_pPSUO2 insolico UniProt ID   Q5JBL6
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14456.50 Da        Isoelectric Point: 5.2973

>WP_000124979.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDGE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB Q5JBL6


T4CP

ID   1831 GenBank   WP_088895587
Name   traC_ACJ74_RS25145_pPSUO2 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99444.28 Da        Isoelectric Point: 6.2641

>WP_088895587.1 type IV secretion system protein TraC [Escherichia coli]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEILGEMSFPQFSRLLPYRDYNQESGLFMNDTTLGFMLEAI
PINGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQY
TAGGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

  Protein structure



No available structure.



ID   1832 GenBank   WP_000009363
Name   traD_ACJ74_RS25830_pPSUO2 insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 84259.95 Da        Isoelectric Point: 5.0504

>WP_000009363.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3524..11114

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ACJ74_RS25150 (ACJ74_24255) 2094..2441 - 348 WP_024233420 hypothetical protein -
ACJ74_RS25155 (ACJ74_24260) 2469..2687 - 219 WP_024233419 hypothetical protein -
ACJ74_RS25160 (ACJ74_24265) 2767..3240 - 474 WP_000549600 hypothetical protein -
ACJ74_RS25165 (ACJ74_24270) 3233..3406 - 174 WP_024262213 conjugal transfer protein TraR -
ACJ74_RS25170 (ACJ74_24275) 3524..4039 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
ACJ74_RS25175 (ACJ74_24280) 4036..4287 - 252 WP_001038341 conjugal transfer protein TrbG -
ACJ74_RS25180 (ACJ74_24285) 4284..4601 - 318 WP_001057292 conjugal transfer protein TrbD virb4
ACJ74_RS25185 (ACJ74_24290) 4598..5170 - 573 WP_000002794 conjugal transfer pilus-stabilizing protein TraP -
ACJ74_RS25190 (ACJ74_24295) 5160..6587 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
ACJ74_RS25195 (ACJ74_24300) 6587..7315 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
ACJ74_RS25200 (ACJ74_24305) 7302..7868 - 567 WP_011251373 type IV conjugative transfer system protein TraE traE
ACJ74_RS25205 (ACJ74_24310) 7890..8201 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
ACJ74_RS25210 (ACJ74_24315) 8216..8575 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
ACJ74_RS25215 (ACJ74_24320) 8609..8836 - 228 WP_001254385 conjugal transfer relaxosome protein TraY -
ACJ74_RS25220 (ACJ74_24325) 8930..9616 - 687 WP_000332493 PAS domain-containing protein -
ACJ74_RS25225 (ACJ74_24330) 9807..10190 - 384 WP_000124979 conjugal transfer relaxosome DNA-binding protein TraM -
ACJ74_RS25230 (ACJ74_24335) 10467..11114 + 648 WP_000615259 transglycosylase SLT domain-containing protein virB1
ACJ74_RS25235 (ACJ74_24340) 11411..12232 - 822 WP_001234469 DUF932 domain-containing protein -
ACJ74_RS25240 (ACJ74_24345) 12352..12639 - 288 WP_000107535 hypothetical protein -
ACJ74_RS26365 (ACJ74_24350) 12664..12870 - 207 WP_000547971 hypothetical protein -
ACJ74_RS26775 12940..13113 + 174 Protein_21 hypothetical protein -
ACJ74_RS26780 13111..13341 - 231 WP_001426396 hypothetical protein -
ACJ74_RS25255 (ACJ74_24365) 13560..13685 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
ACJ74_RS26785 13627..13776 - 150 Protein_24 plasmid maintenance protein Mok -
ACJ74_RS26215 (ACJ74_24370) 13798..13986 + 189 WP_001299721 hypothetical protein -
ACJ74_RS25260 (ACJ74_24375) 13955..14717 - 763 Protein_26 plasmid SOS inhibition protein A -
ACJ74_RS25265 (ACJ74_24380) 14714..15148 - 435 WP_000845873 conjugation system SOS inhibitor PsiB -

Region 2: 95281..109914

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ACJ74_RS25830 (ACJ74_24870) 95281..97506 - 2226 WP_000009363 type IV conjugative transfer system coupling protein TraD virb4
ACJ74_RS25835 (ACJ74_24875) 97759..98490 - 732 WP_123058016 conjugal transfer complement resistance protein TraT -
ACJ74_RS25840 (ACJ74_24880) 98522..99025 - 504 WP_000605510 hypothetical protein -
ACJ74_RS25845 (ACJ74_24885) 99040..101861 - 2822 Protein_118 conjugal transfer mating-pair stabilization protein TraG -
ACJ74_RS25850 (ACJ74_24890) 101858..103231 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
ACJ74_RS25855 (ACJ74_24895) 103231..103593 - 363 WP_011251381 P-type conjugative transfer protein TrbJ -
ACJ74_RS25860 (ACJ74_24900) 103523..104068 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
ACJ74_RS25865 (ACJ74_24905) 104055..104339 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
ACJ74_RS25870 (ACJ74_24910) 104458..104805 - 348 WP_011251380 conjugal transfer protein TrbA -
ACJ74_RS25875 (ACJ74_24915) 104821..105564 - 744 WP_001030390 type-F conjugative transfer system pilin assembly protein TraF traF
ACJ74_RS25880 (ACJ74_24920) 105557..105814 - 258 WP_000864328 conjugal transfer protein TrbE -
ACJ74_RS25885 (ACJ74_24925) 105841..107649 - 1809 WP_011251379 type-F conjugative transfer system mating-pair stabilization protein TraN traN
ACJ74_RS25890 (ACJ74_24930) 107646..108284 - 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
ACJ74_RS25895 (ACJ74_24935) 108293..109285 - 993 WP_001712363 conjugal transfer pilus assembly protein TraU traU
ACJ74_RS25900 (ACJ74_24940) 109282..109914 - 633 WP_011251377 type-F conjugative transfer system protein TraW traW
ACJ74_RS25905 (ACJ74_24945) 109911..110297 - 387 WP_011251376 type-F conjugative transfer system protein TrbI -

Host bacterium

ID   3325 GenBank   NZ_CP011916
Plasmid name   pPSUO2 Incompatibility group   IncFIB
Plasmid size   110961 bp Coordinate of oriT [Strand]   10419..10542 [-]
Host baterium   Escherichia coli strain PSUO2

Cargo genes

Drug resistance gene   sitABCD
Virulence gene   iroB, iroC, iroD, iroE, iroN
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -