Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105194
Name   oriT_pRHB28-C13_2 in_silico
Organism   Escherichia fergusonii strain RHB28-C13
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055676 (200573..200826 [-], 254 nt)
oriT length   254 nt
IRs (inverted repeats)      152..157, 159..164  (AAAAGT..ACTTTT)
 121..129, 134..142  (TTAAGGCTT..AAGCCTTAA)
 50..55, 59..64  (AATTTT..AAAATT)
Location of nic site      77..78
Conserved sequence flanking the
  nic site    		  TTTGGTTAAA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 254 nt

>oriT_pRHB28-C13_2
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3580 GenBank   WP_228728448
Name   mobH_HVY52_RS23835_pRHB28-C13_2 insolico UniProt ID   _
Length   1050 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1050 a.a.        Molecular weight: 118061.46 Da        Isoelectric Point: 4.5894

>WP_228728448.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDT
VETAVLKVNDLGRSTASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVG
SCATSSSVHNEKLLPEPSELPELNREQNADPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGYNLNSKVFATTESDQNGEFSLISEGDVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(108-304)


  Protein structure



No available structure.




T4CP

ID   3543 GenBank   WP_001284076
Name   traD_HVY52_RS23840_pRHB28-C13_2 insolico UniProt ID   _
Length   694 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 694 a.a.        Molecular weight: 78137.93 Da        Isoelectric Point: 8.0177

>WP_001284076.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANETLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH

  Protein domains


Predicted by InterproScan.

AAA-like domain (AAA_10)

(199-249)

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

(406-609)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2429..11636

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HVY52_RS22805 (HVY52_22790) 1..876 + 876 WP_000594612 RepB family plasmid replication initiator protein -
HVY52_RS22810 (HVY52_22795) 2025..2378 + 354 WP_000423602 hypothetical protein -
HVY52_RS22815 (HVY52_22800) 2429..2746 + 318 WP_000043357 type IV conjugative transfer system protein TraL traL
HVY52_RS22820 (HVY52_22805) 2758..3546 + 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
HVY52_RS22825 (HVY52_22810) 3546..4817 + 1272 WP_042634271 type-F conjugative transfer system secretin TraK traK
HVY52_RS22830 (HVY52_22815) 4819..5280 + 462 WP_042634272 plasmid transfer protein HtdO -
HVY52_RS22835 (HVY52_22820) 5270..6625 + 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
HVY52_RS22840 (HVY52_22825) 6633..7115 + 483 WP_000377633 hypothetical protein -
HVY52_RS22845 (HVY52_22830) 7234..7986 + 753 WP_183079335 protein-disulfide isomerase HtdT -
HVY52_RS22850 (HVY52_22835) 7996..8946 + 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
HVY52_RS22855 (HVY52_22840) 8955..11636 + 2682 WP_000387412 TraC family protein virb4
HVY52_RS22860 (HVY52_22845) 14726..15979 + 1254 WP_032084678 ParA family protein -

Host bacterium

ID   5632 GenBank   NZ_CP055676
Plasmid name   pRHB28-C13_2 Incompatibility group   IncHI2A
Plasmid size   282651 bp Coordinate of oriT [Strand]   200573..200826 [-]
Host baterium   Escherichia fergusonii strain RHB28-C13

Cargo genes

Drug resistance gene   aph(6)-Id, aph(3'')-Ib, tet(B), blaTEM-1B, aph(3')-Ia, aac(3)-IVa, aph(4)-Ia, sul3, ant(3'')-Ia, cmlA1, aadA2, tet(A), dfrA12, qacE, sul1, aph(3')-IIa
Virulence gene   -
Metal resistance gene   terW, terZ, terA, terB, terC, terD, terE, silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -