Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103065
Name   oriT_pYD786-1 in_silico
Organism   Escherichia coli strain YD786
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU254578 (56350..56603 [+], 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_pYD786-1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2294 GenBank   WP_000980119
Name   TraI_2_HTG91_RS00305_pYD786-1 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   2004 GenBank   WP_001284076
Name   traD_HTG91_RS00300_pYD786-1 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: 200197..210742

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTG91_RS01035 200197..202878 - 2682 WP_000387412 TraC family protein virb4
HTG91_RS01040 202887..203837 - 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
HTG91_RS01045 203847..204599 - 753 WP_183079335 protein-disulfide isomerase HtdT -
HTG91_RS01050 204718..204882 - 165 WP_236922170 htdV -
HTG91_RS01055 204934..206142 + 1209 WP_001339197 IS4-like element ISVsa5 family transposase -
HTG91_RS01060 206152..206538 - 387 WP_236922171 transcriptional regulator -
HTG91_RS01065 206546..207901 - 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
HTG91_RS01070 207891..208352 - 462 WP_000521240 plasmid transfer protein HtdO -
HTG91_RS01075 208354..209625 - 1272 WP_000592090 type-F conjugative transfer system secretin TraK traK
HTG91_RS01080 209625..210413 - 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
HTG91_RS01085 210425..210742 - 318 WP_000043357 type IV conjugative transfer system protein TraL traL
HTG91_RS01090 210793..211146 - 354 WP_000423602 hypothetical protein -
HTG91_RS01095 212295..213170 - 876 WP_000594612 RepB family plasmid replication initiator protein -
HTG91_RS01100 213647..214702 + 1056 WP_001065779 hypothetical protein -
HTG91_RS01105 214720..214920 + 201 WP_000594931 hypothetical protein -
HTG91_RS01110 214917..215633 + 717 WP_000838218 zinc finger-like domain-containing protein -

Host bacterium

ID   3508 GenBank   NZ_KU254578
Plasmid name   pYD786-1 Incompatibility group   -
Plasmid size   226580 bp Coordinate of oriT [Strand]   56350..56603 [+]
Host baterium   Escherichia coli strain YD786

Cargo genes

Drug resistance gene   sul1, blaCTX-M-2, qacE, aadA2, dfrA12, aph(3'')-Ib, aph(6)-Id
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE, terE, terD, terC, terB, terA, terZ, terW
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -