Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104553
Name   oriT_STLEFF_34|unnamed3 in_silico
Organism   Shigella flexneri strain STLEFF_34
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP058842 (6836..7184 [-], 349 nt)
oriT length   349 nt
IRs (inverted repeats)      134..140, 154..160  (AAAATAT..ATATTTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 349 nt

>oriT_STLEFF_34|unnamed3
ACTGCGATGCAGGATAGGGCAAACGCCGCAAAATGACGTCTCTGACGCCATTCCGCAACGTTTGCCCGGTGACCTACAGTCGGTTCTTGTTGGAGAATTTTATGAAATATTTGGTCAAAGAGTTTATTAACGAAAAATATACTAAGGCTGTTAATATTTTAAAGGATAACCTTAAAGAACACTATCATGTTTTTTATTGTGTGAGATTAAGTGAGATTCTTTTTCCTGCCAGTGAATATGGAACTGAACAGTTTTTTAGTGATTTTGAAAAGATAAACTCCATTTCATTACCTGTCTTAGTGTTTGATCTCAAAGAGGGTGTTCCTGTGATTGTCATTAGTCTTGATGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3282 GenBank   WP_000539530
Name   Relaxase_HZT26_RS24450_STLEFF_34|unnamed3 insolico UniProt ID   A0A611DMI3
Length   388 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 388 a.a.        Molecular weight: 44497.84 Da        Isoelectric Point: 10.5286

>WP_000539530.1 MULTISPECIES: MobP1 family relaxase [Enterobacteriaceae]
MGVYVDKEHRVKRKSSENGRKSAFAHKVKNGGKNYSRNVQERINRKGASKEVVVKISGGAVTRQGIRNSI
DYMSRESELPVMSESGRVWTGDEILEAKEHMIDRANDPQHVMNDKGKENKKITQNIVFSPPVSAKVKPED
LLESVRKTMQKKYPNHRFVLGYHCDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKLKGYD
VKATHKQQHGLNQSVKDAHNTAPKRQKGVYEVVDIGYDHYQNDKTKSKQHFIKLKTLNKGVEKTYWGADF
GDLCSRESVKAGDLVRLKKLGQKEVKIPALDKNGVQHGWKTVHRNEWQLENLGVKGVDRTPSASKELVLN
SPDMLLKQQQRMAQFTQQKASTLQSEQKLKTGIKFFNI

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(70-228)


  Protein structure


Source ID Structure
AlphaFold DB A0A611DMI3


T4CP

ID   3218 GenBank   WP_072107035
Name   t4cp2_HZT26_RS24480_STLEFF_34|unnamed3 insolico UniProt ID   _
Length   664 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 664 a.a.        Molecular weight: 75523.85 Da        Isoelectric Point: 5.7323

>WP_072107035.1 MULTISPECIES: AAA family ATPase [Enterobacteriaceae]
MNEICDRLNTYLSRFHSRRLGLYEDHGVVYSDQLSLFQYLLSGRWQKVRVSSSPFYTYLGGKDLFFGNDA
GQITASDHARYFRCIEIKDYFQETDAGILDALMYLPVEYVVTSSFTAMDKQSAIKALDDQIDKLEMTDDA
AKSLLADLKVGLDMVSSGYISFGKSHQTLVVFADSPERLVKDTNIVTSTLEDLGLIVTYSTLSLGAAYFA
QLPGNYTLRPRLSTLSSLNFAEMESFHNFFSGKEKGNTWGEKLITLRGSGNDIYHLNYHMTTEHQNFFGK
NPTLGHTEILGTSNVGKTVLLMTKAFAAQQFGTPESFPANRKLKKLTTVFFDKDRAGEVGIRAMGGSYYR
VKEGEPTGWNPAALPPTKRNIAFMKDLVRLLCTLNSEPLDDYQNSLISDAVERLMQRSDRSYPISKLRPL
IQEPDDTETKRHGLKARLKPWTQGEEFGWVFDNREDTFDVDNLDVFGIDGTEFLDNKVLASAASFYLIYR
VTMLADGRRLLIYMDEFWQWINNEAFRDFVYNKLKTGRKLDMVLVVATQSPDELIKSPIAAAVREQCATH
IYLANPKAKRSEYVDGLQVRELYFDKIKAIDPLSRQFLVVKNPQRKGESDDFAAFARLELGKAAYYLPVL
SASKPQLELFDEIWKEGMKPEEWLDTYLEQANLI

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(19-221)

  Protein structure



No available structure.



ID   3219 GenBank   WP_031942379
Name   t4cp2_HZT26_RS24525_STLEFF_34|unnamed3 insolico UniProt ID   _
Length   611 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 611 a.a.        Molecular weight: 69331.19 Da        Isoelectric Point: 7.4340

>WP_031942379.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacteriaceae]
MSLKLPDKGQWAFIGLVMCLVTYYTGSVAVYFLNGKTPLYIWKNFDSMLLWRIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFIIWQLNKTDVALYGDAKFASDNDLRKSKLLKWEKENDTGILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREILLGNKVYLLDPFNSKTHQFNPLF
YIDLKAESGAKDLLKLIEILFPSYGMTGAEAHFNNLAGQYWTGLAKLLHFFINYEPSWLNEFGLKPVFSI
GSVVDLYSNIDRELILSKREELEGTNGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDISLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGIEGAKTLMSAHPCRIIYAVSEEDDAAKIS
EKLGYITTTSKSTSKSRGRSTSQGESESEARRALVLPQELGTLDFKEEFIILKGENPVKAEKALYYLDPY
FMDRLMKVSPKLASLTMELNKTKKIFGVKGLKYPSKEKMLSVGELESEVLL

  Protein domains


Predicted by InterproScan.

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

(102-571)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15489..25441

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HZT26_RS24415 (HZT26_24220) 10812..11057 + 246 WP_000356546 hypothetical protein -
HZT26_RS24420 (HZT26_24225) 11047..11262 + 216 WP_001180116 hypothetical protein -
HZT26_RS24425 (HZT26_24230) 11355..11684 + 330 WP_000866648 hypothetical protein -
HZT26_RS24430 (HZT26_24235) 11727..11906 + 180 WP_000439078 hypothetical protein -
HZT26_RS24435 (HZT26_24240) 11976..12125 + 150 WP_000003880 hypothetical protein -
HZT26_RS24440 (HZT26_24245) 12138..12410 + 273 WP_000160399 hypothetical protein -
HZT26_RS24445 (HZT26_24255) 12736..13281 + 546 WP_015060502 DNA distortion polypeptide 1 -
HZT26_RS24450 (HZT26_24260) 13284..14450 + 1167 WP_000539530 MobP1 family relaxase -
HZT26_RS24455 (HZT26_24265) 14796..15314 + 519 WP_001446885 transcription termination/antitermination NusG family protein -
HZT26_RS24460 (HZT26_24270) 15244..15456 + 213 WP_032312290 hypothetical protein -
HZT26_RS24465 (HZT26_24275) 15489..16136 + 648 WP_000953529 lytic transglycosylase domain-containing protein virB1
HZT26_RS24470 (HZT26_24280) 16114..16410 + 297 WP_000916182 TrbC/VirB2 family protein virB2
HZT26_RS24480 (HZT26_24285) 16429..19182 + 2754 WP_001328100 VirB3 family type IV secretion system protein -
HZT26_RS24485 (HZT26_24290) 19193..19942 + 750 WP_000744202 type IV secretion system protein -
HZT26_RS24490 (HZT26_24295) 19957..20241 + 285 WP_000748128 EexN family lipoprotein -
HZT26_RS24495 (HZT26_24300) 20253..21314 + 1062 WP_000796673 type IV secretion system protein virB6
HZT26_RS24505 (HZT26_24305) 21559..22272 + 714 WP_000394613 type IV secretion system protein virB8
HZT26_RS24510 (HZT26_24310) 22277..23206 + 930 WP_000783379 TrbG/VirB9 family P-type conjugative transfer protein virB9
HZT26_RS24515 (HZT26_24315) 23203..24408 + 1206 WP_000139139 VirB10/TraB/TrbI family type IV secretion system protein virB10
HZT26_RS24520 (HZT26_24320) 24410..25441 + 1032 WP_001058463 P-type DNA transfer ATPase VirB11 virB11
HZT26_RS24525 (HZT26_24325) 25444..27279 + 1836 WP_031942379 type IV secretory system conjugative DNA transfer family protein -
HZT26_RS24530 (HZT26_24330) 27276..27689 + 414 WP_031942378 cag pathogenicity island Cag12 family protein -
HZT26_RS24535 (HZT26_24335) 27686..27988 + 303 WP_000717624 TrbM/KikA/MpfK family conjugal transfer protein -
HZT26_RS24540 (HZT26_24340) 28103..29026 - 924 WP_031942377 SMEK domain-containing protein -

Host bacterium

ID   4992 GenBank   NZ_CP058842
Plasmid name   STLEFF_34|unnamed3 Incompatibility group   IncX1
Plasmid size   39202 bp Coordinate of oriT [Strand]   6836..7184 [-]
Host baterium   Shigella flexneri strain STLEFF_34

Cargo genes

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