Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114373
Name   oriT_pYps.R2 in_silico
Organism   Yersinia pseudotuberculosis strain Yps.R2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LT221038 (24644..24744 [+], 101 nt)
oriT length   101 nt
IRs (inverted repeats)      80..85, 91..96  (AAAAAA..TTTTTT)
 20..26, 38..44  (TAAATCA..TGATTTA)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 101 nt

>oriT_pYps.R2
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9214 GenBank   WP_012561166
Name   mobF_BN866_RS00090_pYps.R2 insolico UniProt ID   D7RU03
Length   1078 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120141.30 Da        Isoelectric Point: 6.5229

>WP_012561166.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure


Source ID Structure
AlphaFold DB D7RU03


Auxiliary protein

ID   5400 GenBank   WP_001749975
Name   WP_001749975_pYps.R2 insolico UniProt ID   A0A5C2CVS6
Length   138 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15332.60 Da        Isoelectric Point: 5.9670

>WP_001749975.1 MULTISPECIES: hypothetical protein [Gammaproteobacteria]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A5C2CVS6


T4CP

ID   10680 GenBank   WP_000342688
Name   t4cp2_BN866_RS00095_pYps.R2 insolico UniProt ID   _
Length   509 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 509 a.a.        Molecular weight: 57762.87 Da        Isoelectric Point: 9.6551

>WP_000342688.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI

  Protein domains


Predicted by InterproScan.

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

(113-489)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60738..71067

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BN866_RS00295 56930..58039 + 1110 WP_000842134 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase -
BN866_RS00300 58061..58483 + 423 Protein_58 alpha/beta hydrolase-fold protein -
BN866_RS00305 58529..59233 - 705 WP_001067855 IS6-like element IS26 family transposase -
BN866_RS00310 59298..59477 - 180 Protein_60 ArsR/SmtB family transcription factor -
BN866_RS00445 59744..60031 + 288 Protein_61 DUF6710 family protein -
BN866_RS00325 60205..60738 - 534 WP_000792636 phospholipase D family protein -
BN866_RS00330 60738..61733 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
BN866_RS00335 61775..62935 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
BN866_RS00340 62935..63819 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
BN866_RS00345 63830..64528 - 699 WP_000646594 virB8 family protein virB8
BN866_RS00350 64518..64676 - 159 WP_012561180 hypothetical protein -
BN866_RS00355 64747..65787 - 1041 WP_001749958 type IV secretion system protein virB6
BN866_RS00360 65803..66030 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
BN866_RS00365 66038..66802 - 765 WP_013149461 type IV secretion system protein virB5
BN866_RS00370 66769..69369 - 2601 WP_012561149 VirB4 family type IV secretion/conjugal transfer ATPase virb4
BN866_RS00375 69369..69686 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
BN866_RS00380 69737..70030 - 294 WP_001749962 hypothetical protein virB2
BN866_RS00385 70040..70321 - 282 WP_016338364 transcriptional repressor KorA -
BN866_RS00390 70330..71067 - 738 WP_013279384 lytic transglycosylase domain-containing protein virB1
BN866_RS00395 71104..71481 + 378 WP_193567606 H-NS family nucleoid-associated regulatory protein -
BN866_RS00400 71497..71841 + 345 WP_012561155 hypothetical protein -
BN866_RS00405 71838..72152 + 315 WP_016338363 TrbM/KikA/MpfK family conjugal transfer protein -
BN866_RS00410 72188..72499 + 312 WP_013279382 hypothetical protein -
BN866_RS00415 72555..73196 + 642 WP_012561158 restriction endonuclease -
BN866_RS00420 73201..73407 + 207 WP_001749967 hypothetical protein -
BN866_RS00425 73418..73690 - 273 Protein_82 IS1 family transposase -
BN866_RS00430 73789..75222 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   14808 GenBank   NZ_LT221038
Plasmid name   pYps.R2 Incompatibility group   IncN
Plasmid size   76709 bp Coordinate of oriT [Strand]   24644..24744 [+]
Host baterium   Yersinia pseudotuberculosis strain Yps.R2

Cargo genes

Drug resistance gene   aph(3'')-Ib, aph(6)-Id, sul2, tet(D)
Virulence gene   -
Metal resistance gene   arsR, arsD, arsA, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -