Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111117
Name   oriT_pYps.R1 in_silico
Organism   Yersinia pseudotuberculosis strain Yps.R1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LT221037 (13790..13890 [-], 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.R1
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7289 GenBank   WP_012561166
Name   mobF_HXI22_RS00110_pYps.R1 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   4055 GenBank   WP_001749975
Name   WP_001749975_pYps.R1 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   8306 GenBank   WP_000342688
Name   t4cp2_HXI22_RS00105_pYps.R1 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: 38356..48681

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXI22_RS00205 34548..35657 + 1110 WP_000842134 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase -
HXI22_RS00210 35679..36101 + 423 Protein_41 alpha/beta hydrolase-fold protein -
HXI22_RS00215 36147..36851 - 705 WP_001067855 IS6-like element IS26 family transposase -
HXI22_RS00220 36916..37095 - 180 Protein_43 helix-turn-helix domain-containing protein -
HXI22_RS00230 37521..37649 + 129 WP_002210551 DUF6710 family protein -
HXI22_RS00235 37823..38356 - 534 WP_176454444 phospholipase D family protein -
HXI22_RS00240 38356..39351 - 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HXI22_RS00245 39393..40553 - 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HXI22_RS00250 40553..41437 - 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HXI22_RS00255 41448..42146 - 699 WP_000646594 type IV secretion system protein virB8
HXI22_RS00260 42136..42294 - 159 WP_012561180 hypothetical protein -
HXI22_RS00265 42365..43405 - 1041 WP_001749958 type IV secretion system protein virB6
HXI22_RS00270 43421..43648 - 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HXI22_RS00275 43656..44420 - 765 WP_013149461 type IV secretion system protein virB5
HXI22_RS00280 44387..46987 - 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXI22_RS00285 46987..47304 - 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HXI22_RS00290 47354..47647 - 294 WP_001749962 hypothetical protein virB2
HXI22_RS00295 47657..47938 - 282 WP_000440698 transcriptional repressor KorA -
HXI22_RS00300 47947..48681 - 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HXI22_RS00305 48724..49095 + 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HXI22_RS00310 49111..49455 + 345 WP_001749964 hypothetical protein -
HXI22_RS00315 49452..49766 + 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HXI22_RS00320 49880..50113 + 234 WP_001191790 hypothetical protein -
HXI22_RS00325 50163..50810 + 648 WP_015344958 restriction endonuclease -
HXI22_RS00330 50815..51021 + 207 WP_001749967 hypothetical protein -
HXI22_RS00335 51032..51304 - 273 Protein_65 IS1 family transposase -
HXI22_RS00340 51403..52836 + 1434 WP_001288432 DNA cytosine methyltransferase -

Host bacterium

ID   11552 GenBank   NZ_LT221037
Plasmid name   pYps.R1 Incompatibility group   IncN
Plasmid size   60299 bp Coordinate of oriT [Strand]   13790..13890 [-]
Host baterium   Yersinia pseudotuberculosis strain Yps.R1

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, catA2, tet(D), dfrA14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -