Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100140
Name   oriT2_pMAS2027 experimental
Organism   Escherichia coli
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_013503 ( 38362..38380 [+], 19 nt)
oriT length   19 nt
IRs (inverted repeats)     _
Location of nic site      13..14
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   _

  oriT sequence  


Download         Length: 19 nt

>oriT2_pMAS2027
TTGCCCTATCCTGCATCGC

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Ong CL et al. (2009) Conjugative plasmid transfer and adhesion dynamics in an Escherichia coli biofilm. Appl Environ Microbiol. 75(21):6783-91. [PMID:19717626]


Relaxase

ID   134 GenBank   YP_003292208
Name   TaxC_pMAS2027 insolico UniProt ID   D0QMQ2
Length   390 a.a. PDB ID   
Note   Relaxase

  Relaxase protein sequence


Download         Length: 390 a.a.        Molecular weight: 44752.18 Da        Isoelectric Point: 10.5067

>YP_003292208.1 TaxC (plasmid) [Escherichia coli]
MIMGVYVDKEYRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAVTRQGIRN
SIDYMSRESELPVMSESGRVWTGDEILEAKDHMIDRANDPQHVMNDKGKENKKITQNIVFSPPVSAKVKP
EDLLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKG
YDVKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDVGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGA
DFGDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELV
LNSPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFWSL

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(72-231)


  Protein structure


Source ID Structure
AlphaFold DB D0QMQ2

  Reference


[1] Ong CL et al. (2009) Conjugative plasmid transfer and adhesion dynamics in an Escherichia coli biofilm. Appl Environ Microbiol. 75(21):6783-91. [PMID:19717626]


Auxiliary protein

ID   197 GenBank   YP_003292209
Name   Ddp1_pMAS2027 insolico UniProt ID   D0QMQ3
Length   204 a.a. PDB ID   _
Note   similar to TaxA from R6K

  Auxiliary protein sequence


Download         Length: 204 a.a.        Molecular weight: 24091.59 Da        Isoelectric Point: 8.0185

>YP_003292209.1 DNA distortion polypeptide 1 (plasmid) [Escherichia coli]
MTSMTPFRNVCPVTYSRFFLENFMKKVQFRIDENQHDDLLDCLKTLYPDEPALTVAKGMKLLANALLKSK
AGSKDINTFFDNNDFIKTTMYLTGKQRADIERAANRHGWTLSRECRYRIQTTLENELDFFDQELLMMNRC
RNSIDKIGRNFHYIIVNDQTRVLDKDGFYQDAERLTTEIFNLKNQFENYIMLCKGRTVSNKVEM

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB D0QMQ3

  Reference


[1] Ong CL et al. (2009) Conjugative plasmid transfer and adhesion dynamics in an Escherichia coli biofilm. Appl Environ Microbiol. 75(21):6783-91. [PMID:19717626]


T4CP

ID   134 GenBank   YP_003292195
Name   TaxB_pMAS2027 insolico UniProt ID   D0QMN9
Length   613 a.a. PDB ID   _
Note   bacterial conjugative protein involved in type IV sectretion

  T4CP protein sequence


Download         Length: 613 a.a.        Molecular weight: 69645.64 Da        Isoelectric Point: 7.1491

>YP_003292195.1 TaxB (plasmid) [Escherichia coli]
MIMSLKLPDKGQWAFIGLVMCLVTYYTGSVAVYFLNGKTPLYIWKNFDSMLLWRIITESNIRIDIRLTAI
PSLLSGMVSSLIVPVFIIWQLNKTDVALYGDAKFASDNDLRKSKLLKWEKENDTDILVGAYKGKYLWYTA
PDFVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREILLGNKVYLLDPFNSKTHQFNP
LFYIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYEPSWLNEFGLKPVF
SIGSVVDLYSNIDRELILSKREELEGTNGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLF
YLPTVRKCTDGNDFDLRQLRREDITVYVGVNAEDISLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLM
FLDEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAAK
ISEKLGYITTTSKSTSKSRGRSTSQGESESEARRALVLPQELGTLDFKEEFIILKGENPVKAEKALYYLD
PYFMDRLMKVSPKLASLTMELNKTKKIFGVKGLKYPSKEKMLSVGELESEVLL

  Protein domains


Predicted by InterproScan.

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

(104-573)

  Protein structure


Source ID Structure
AlphaFold DB D0QMN9

  Reference


[1] Ong CL et al. (2009) Conjugative plasmid transfer and adhesion dynamics in an Escherichia coli biofilm. Appl Environ Microbiol. 75(21):6783-91. [PMID:19717626]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 25562..35522

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS641_RS00130 (pMAS2027_32) 21935..22900 + 966 WP_001328098 SMEK domain-containing protein -
HS641_RS00135 (pMAS2027_33) 23015..23317 - 303 WP_000717624 TrbM/KikA/MpfK family conjugal transfer protein -
HS641_RS00140 (pMAS2027_34) 23314..23727 - 414 WP_000722603 cag pathogenicity island Cag12 family protein -
HS641_RS00145 (pMAS2027_35) 23724..25559 - 1836 WP_014106755 type IV secretory system conjugative DNA transfer family protein -
HS641_RS00150 (pMAS2027_36) 25562..26593 - 1032 WP_001058465 P-type DNA transfer ATPase VirB11 virB11
HS641_RS00155 (pMAS2027_37) 26595..27800 - 1206 WP_000139139 VirB10/TraB/TrbI family type IV secretion system protein virB10
HS641_RS00160 (pMAS2027_38) 27797..28726 - 930 WP_000783379 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS641_RS00165 (pMAS2027_39) 28731..29444 - 714 WP_000394615 type IV secretion system protein virB8
HS641_RS00270 (pMAS2027_40) 29434..29562 - 129 WP_001328099 hypothetical protein -
HS641_RS00170 (pMAS2027_41) 29689..30822 - 1134 WP_000513457 type IV secretion system protein virB6
HS641_RS00175 (pMAS2027_42) 30832..31059 - 228 WP_000835349 EexN family lipoprotein -
HS641_RS00180 (pMAS2027_43) 31060..31818 - 759 WP_000744200 type IV secretion system protein -
HS641_RS00185 (pMAS2027_44) 31829..34582 - 2754 WP_001352869 VirB3 family type IV secretion system protein virb4
HS641_RS00190 (pMAS2027_45) 34601..34897 - 297 WP_000916182 TrbC/VirB2 family protein virB2
HS641_RS00195 (pMAS2027_46) 34875..35522 - 648 WP_000953526 lytic transglycosylase domain-containing protein virB1
HS641_RS00200 35555..35767 - 213 WP_000125172 hypothetical protein -
HS641_RS00205 (pMAS2027_47) 35697..36215 - 519 WP_001446885 transcription termination/antitermination NusG family protein -
HS641_RS00210 (pMAS2027_48) 36568..37734 - 1167 WP_000539538 MobP1 family relaxase -
HS641_RS00215 (pMAS2027_49) 37737..38282 - 546 WP_001426313 DNA distortion polypeptide 1 -
HS641_RS00225 (pMAS2027_51) 38608..38880 - 273 WP_000167280 hypothetical protein -
HS641_RS00230 38897..39091 - 195 WP_001714231 hypothetical protein -
HS641_RS00275 39113..39292 - 180 WP_024133577 hypothetical protein -
HS641_RS00235 (pMAS2027_52) 39335..39664 - 330 WP_000866654 hypothetical protein -
HS641_RS00240 (pMAS2027_53) 39758..40000 - 243 WP_000008708 hypothetical protein -
HS641_RS00245 (pMAS2027_54) 39990..40271 - 282 WP_012845398 hypothetical protein -

Host bacterium

ID   134 GenBank   NC_013503
Plasmid name   pMAS2027 Incompatibility group   IncX1
Plasmid size   42644 bp Coordinate of oriT [Strand]   2060..2078 [-]; 38362..38380 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   -
Virulence gene   mrkF, mrkD, mrkC, mrkB, mrkA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -