Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104180
Name   oriT_pKLO00003_2 in_silico
Organism   Klebsiella oxytoca strain KLO00003
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OP378638 (231844..232098 [-], 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_pKLO00003_2
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGCAGGAATTTTTGATAAAATTCTGGTTAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3072 GenBank   WP_012477394
Name   mobH_PWC54_RS01225_pKLO00003_2 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   2967 GenBank   WP_001284073
Name   traD_PWC54_RS01230_pKLO00003_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: 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: 2429..11636

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PWC54_RS00005 1..876 + 876 WP_000594611 RepB family plasmid replication initiator protein -
PWC54_RS00010 2025..2378 + 354 WP_000423602 hypothetical protein -
PWC54_RS00015 2396..2746 + 351 WP_001447770 type IV conjugative transfer system protein TraL -
PWC54_RS00020 2758..3546 + 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
PWC54_RS00025 3546..4817 + 1272 WP_000592092 type-F conjugative transfer system secretin TraK traK
PWC54_RS00030 4819..5280 + 462 WP_000521242 plasmid transfer protein HtdO -
PWC54_RS00035 5270..6625 + 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
PWC54_RS00040 6633..7115 + 483 WP_000377632 hypothetical protein -
PWC54_RS00045 7234..7986 + 753 WP_182911723 protein-disulfide isomerase HtdT -
PWC54_RS00050 7996..8946 + 951 WP_001022588 IncHI-type conjugal transfer lipoprotein TrhV traV
PWC54_RS00055 8955..11636 + 2682 WP_000387412 TraC family protein virb4

Host bacterium

ID   4619 GenBank   NZ_OP378638
Plasmid name   pKLO00003_2 Incompatibility group   IncHI2A
Plasmid size   304642 bp Coordinate of oriT [Strand]   231844..232098 [-]
Host baterium   Klebsiella oxytoca strain KLO00003

Cargo genes

Drug resistance gene   tet(A), dfrA14, qnrB1, aac(6')-Ib-cr, blaOXA-1, blaCTX-M-15, blaTEM-1B, aph(6)-Id, aph(3'')-Ib, sul2, ant(3'')-Ia, catA1
Virulence gene   -
Metal resistance gene   terW, terZ, terA, terB, terC, terD, terE, merD, merE, pcoE, ncrC, rcnR/yohL, arsC, arsB, arsR, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -