Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113154
Name   oriT_p30038n1 in_silico
Organism   Escherichia fergusonii strain 30038
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP027927 (166831..167084 [-], 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_p30038n1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8446 GenBank   WP_000980119
Name   mobH_QUE84_RS23500_p30038n1 insolico UniProt ID   A0A0H3VVI8
Length   1050 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1050 a.a.        Molecular weight: 118035.42 Da        Isoelectric Point: 4.6054

>WP_000980119.1 MULTISPECIES: MobH family relaxase [Enterobacteriaceae]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDT
VETAVLKVNDLGRSTASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVG
SCATSSSVHNEKLLPEPSELPELNREQNADPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFATTESDQNGEFSLISEGDVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(108-304)


  Protein structure


Source ID Structure
AlphaFold DB A0A0H3VVI8


T4CP

ID   9740 GenBank   WP_286356232
Name   traD_QUE84_RS23505_p30038n1 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: 78187.00 Da        Isoelectric Point: 8.0165

>WP_286356232.1 conjugative transfer system coupling protein TraD [Escherichia fergusonii]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIAYLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
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
QUE84_RS22600 (Ef30038_43300) 1..876 + 876 WP_000594612 RepB family plasmid replication initiator protein -
QUE84_RS22605 (Ef30038_43320) 2025..2378 + 354 WP_000423602 hypothetical protein -
QUE84_RS22610 (Ef30038_43330) 2429..2746 + 318 WP_000043357 type IV conjugative transfer system protein TraL traL
QUE84_RS22615 (Ef30038_43340) 2758..3546 + 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
QUE84_RS22620 (Ef30038_43350) 3546..4817 + 1272 WP_000592090 type-F conjugative transfer system secretin TraK traK
QUE84_RS22625 4819..5280 + 462 WP_000521240 plasmid transfer protein HtdO -
QUE84_RS22630 (Ef30038_43370) 5270..6625 + 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
QUE84_RS22635 (Ef30038_43380) 6633..7115 + 483 WP_000377633 hypothetical protein -
QUE84_RS22640 (Ef30038_43390) 7234..7986 + 753 WP_183079335 protein-disulfide isomerase HtdT -
QUE84_RS22645 (Ef30038_43400) 7996..8946 + 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
QUE84_RS22650 (Ef30038_43410) 8955..11636 + 2682 WP_000387412 TraC family protein virb4

Host bacterium

ID   13589 GenBank   NZ_AP027927
Plasmid name   p30038n1 Incompatibility group   IncHI2A
Plasmid size   234318 bp Coordinate of oriT [Strand]   166831..167084 [-]
Host baterium   Escherichia fergusonii strain 30038

Cargo genes

Drug resistance gene   aph(3')-Ia, aph(6)-Id, aph(3'')-Ib, sul2, blaTEM-1B, catA1, tet(A), dfrA12, aadA2, qacE, sul1
Virulence gene   -
Metal resistance gene   terW, terZ, terA, terB, terC, terD, terE, merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -