Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114460
Name   oriT_XY-1|unnamed1 in_silico
Organism   Raoultella sp. XY-1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP067067 (204098..204352 [+], 255 nt)
oriT length   255 nt
IRs (inverted repeats)      153..158, 160..165  (AAAAGT..ACTTTT)
 122..130, 135..143  (TTAAGGCTT..AAGCCTTAA)
 49..55, 60..66  (GAATTTT..AAAATTC)
Location of nic site      78..79
Conserved sequence flanking the
  nic site    		  TTTGGTTAAA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 255 nt

>oriT_XY-1|unnamed1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9270 GenBank   WP_012477394
Name   mobH_JGY86_RS26930_XY-1|unnamed1 insolico UniProt ID   A0A2Z2E7B6
Length   1050 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1050 a.a.        Molecular weight: 118067.47 Da        Isoelectric Point: 4.6347

>WP_012477394.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MMMNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPT
GIQTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGG
LLSHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWT
PSSQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYT
DGNDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGE
VYLNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFR
NGIGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDVITKITDT
VETAVLKVNDLGRSSASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESE
DESAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDTTMALLPGLDEKAFSEEPYFQLTFREGS
LDGMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLE
LPPPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEKEDEEHEIIDYTDFSQLSVSRPEVG
SCATSSSVHNEKLLSEPSELPELNREQNADPQGTNERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAA
ATSVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPAS
PVSGHNLNSKVFASTESDQNGEFSLISEGDVTELEFVEIALVLHQILSKMEVAFKRKRKNRFMVSTPNTL
YLTQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(108-304)


  Protein structure


Source ID Structure
AlphaFold DB A0A2Z2E7B6


T4CP

ID   10749 GenBank   WP_001284073
Name   traD_JGY86_RS26925_XY-1|unnamed1 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: 78123.91 Da        Isoelectric Point: 8.0177

>WP_001284073.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANDTLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKLH

  Protein domains


Predicted by InterproScan.

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

(406-609)

AAA-like domain (AAA_10)

(199-249)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 73432..82639

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JGY86_RS26190 (JGY86_26190) 70722..70883 - 162 WP_001371949 hypothetical protein -
JGY86_RS26195 (JGY86_26195) 73432..76113 - 2682 WP_000387412 TraC family protein virb4
JGY86_RS26200 (JGY86_26200) 76122..77072 - 951 WP_001022588 IncHI-type conjugal transfer lipoprotein TrhV traV
JGY86_RS26205 (JGY86_26205) 77082..77834 - 753 WP_182911723 protein-disulfide isomerase HtdT -
JGY86_RS26210 (JGY86_26210) 77953..78435 - 483 WP_000377632 hypothetical protein -
JGY86_RS26215 (JGY86_26215) 78443..79798 - 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
JGY86_RS26220 (JGY86_26220) 79788..80249 - 462 WP_000521242 plasmid transfer protein HtdO -
JGY86_RS26225 (JGY86_26225) 80251..81522 - 1272 WP_000592092 type-F conjugative transfer system secretin TraK traK
JGY86_RS26230 (JGY86_26230) 81522..82310 - 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
JGY86_RS26235 (JGY86_26235) 82322..82639 - 318 WP_000043358 type IV conjugative transfer system protein TraL traL
JGY86_RS26240 (JGY86_26240) 82690..83043 - 354 WP_000423602 hypothetical protein -
JGY86_RS26245 (JGY86_26245) 84192..84938 - 747 Protein_80 plasmid replication initiator TrfA -
JGY86_RS26250 (JGY86_26250) 84998..86145 + 1148 WP_140392695 IS3 family transposase -
JGY86_RS28435 86162..86299 - 138 Protein_82 protein RepA -

Host bacterium

ID   14895 GenBank   NZ_CP067067
Plasmid name   XY-1|unnamed1 Incompatibility group   IncHI2A
Plasmid size   328379 bp Coordinate of oriT [Strand]   204098..204352 [+]
Host baterium   Raoultella sp. XY-1

Cargo genes

Drug resistance gene   aac(6')-IIc, ere(A), qacE, sul1, qnrB4, blaDHA-1, catA2, tet(D), aph(3')-Ia, aph(6)-Id, aph(3'')-Ib, dfrA17, oqxB, oqxA, floR, sul2
Virulence gene   -
Metal resistance gene   terE, terD, terC, terB, terA, terZ, terW, pcoE, pcoC, silP, silA, silB, silF, silC, silR, silE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -