Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120149
Name   oriT_pLBA3-1 in_silico
Organism   Citrobacter braakii strain LBA3
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP113164 (224808..225061 [-], 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_pLBA3-1
GGATTTAGGTTTTTTTTTAATCGCTTCACATTTCGTTAGCATGCGAAGAAATTTTGATAAAATTCTGGTCAGTTTGGTTAAAAAGTGTTACAAGTAAGCGGTGTGGTTGAAGGGATAGATTTAAGGCTTATTCAAGCCTTAAGAAAATACTAAAAGTTACTTTTCACCCTACCGAACACCTAACAAAAAATCCATGTTGAAGATTTGAACAATTGTAATGGCGCAAGGACAATCAGCACATGTCAGAATCTGAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12679 GenBank   WP_001011151
Name   mobH_MKJ05_RS24795_pLBA3-1 insolico UniProt ID   A0A1P8VU63
Length   1048 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1048 a.a.        Molecular weight: 117773.04 Da        Isoelectric Point: 4.6054

>WP_001011151.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MNFRALYLCIKRILGIFSSQENDATSVMIEDISSLSPFAQILGDQKYTVPDHPNPEVLKFIEYPTRPTGI
QTFNEQSILSLYREKLHSISMMLAISDSDIRDDAYTFTNLVLKPLVEYVRWIHLLPASENHHHNGIGGLL
SHSLEVAILSLKNAHHSELRPIGYQDEEVVRRKVYLYAAFICGLVHDAGKVYDLDIVSLNLASPIIWTPS
SQSLLDWARENDVVEYEIHWRKRIHNQHNIWSSVFLERILNPVCLAFLDRVNKERVYSKMITALNVYTDG
NDFLSKCVRTADFYSTGTDLNVLRDPIMGLRSNDAAARAISTIKHNFTSININNYNAKPMHIIIVNGEVY
LNENAFLDFVLNDFELHKYNFPQGEAGKTVLVESLVQRGYVEPYDDERVVHYFIPGIYSENEISNIFRNG
IGKLEFYNLLKLRWIGLIFDSYKIPDSVPGLFSVNANKDFIYIDEQKTVTEYRRPVPGRDAITKITDTVE
TAVLKVNDLGRSTASIDVDIHSKKNEGSSDDFEKKAESDNEIDNDTQIVKSEGEEAADPVIPDIEESEDE
SAKDTESHVLVNQLHELLLSAPLSNDYIVCVDAVPYLNIDATMALLPGLDEKAFSEEPYFQLTFREGSLD
GMWIVRDIDDLRLVQLGDNCAGFQLTYHEPRRPTTLKSLFNTSMYQALVINDESSVENSAPRPKQTLELP
PPRVNAVEEHSGDVEYHGTDSASATGPLKTEAVEYEHYQHLFEEEDEEHEIIDYTDFTQLSVSRPEVGSC
ATSSSVHNEKLLPEPSELPELNREQNADPQGTIERSMDVSVGQENSEPDTEGNCPPPAEVVYSQTEAAAT
SVMASEEPALPPVLEESNGEHAPTDAKGHHLSPALARLFAPTAPVEKQNPKRNRNKSSDKAEVQKPASPV
SGHNLNSKVFATTESDQNGEFSLISEGDVTELEFVEIASVLHQILSKMEVAFKRKRKNRFMVSTPNTLYL
TQSCVEKFGSQLEAQDLFNKLPQYLVNSGAVINTKCHAFNMPTLLAASDRAKVDIERIINNLKEAGNL

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(106-302)


  Protein structure


Source ID Structure
AlphaFold DB A0A1P8VU63


T4CP

ID   14882 GenBank   WP_046788497
Name   traD_MKJ05_RS24800_pLBA3-1 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: 78171.95 Da        Isoelectric Point: 8.0177

>WP_046788497.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacterales]
MSDSKRTNLHAQENFYRPILEYRSASILLICSVSMLYMGLSSDGLDIAPIVLFTSILLFLLCLYRCKTAA
PFLMAHWRVFKRHFMFVSLDSLRVINKSNFFSNERKYRQLVQDYQNKNKDIPERKSYFCDGFEWGPEHAD
RAYQIANLSSDKREIELPFVFNPIKRHFDAMARKMGGSNAIFAVERREPIFVTEDNWFGHTLITGNVGTG
KTVLQRLLSISMLHLGHVVVVIDPKNDAEWRESLMEEAKTLGLPFYKFHPGQPASSVCIDVCNTYTNVSD
LTSRLLSLVTVPGEVNPFVQYAKALVSNVISGLSYIEKKPSIYLIHKNMKSHMSIVNLTVKVMESCYARY
YGYDVWTEKVKYVANETLPVRFKRLAEWFTAHFMNYEGSEQIDWLDTVSQLIDYSMSDPEHMAKMTAGIM
PVFDMLIEKPLNELLSPNPNSVSSREIVTSEGMFSTGGVLYISLDGLSNPDTAAAISQLIMSDLTSCAGS
RYNAQDGDMSANSRISIFVDEAHSAINNPMINLLAQGRAAKIALFICTQTISDFIAAASVETANRITGLC
NNYISLRVNDTPTQTLVVENFGKSAISTNMVTYTTGSETSLPHNNFSGSISERKQTTLEESIPKDLLGQV
PMFHIVARLQDGRKVVGQIPIAVAEKQMKPNTTLSEMLFKKAGKVTLRQNLDIKNLNKFLRKFH

  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: 61475..70682

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MKJ05_RS23895 (MKJ05_23895) 57698..58573 + 876 WP_000594612 RepB family plasmid replication initiator protein -
MKJ05_RS23900 (MKJ05_23900) 59722..60075 + 354 WP_000423602 hypothetical protein -
MKJ05_RS23905 (MKJ05_23905) 60164..61276 + 1113 WP_001300563 IS4-like element IS421 family transposase -
MKJ05_RS23910 (MKJ05_23910) 61475..61792 + 318 WP_000043357 type IV conjugative transfer system protein TraL traL
MKJ05_RS23915 (MKJ05_23915) 61804..62592 + 789 WP_000783153 TraE/TraK family type IV conjugative transfer system protein traE
MKJ05_RS23920 (MKJ05_23920) 62592..63863 + 1272 WP_000592090 type-F conjugative transfer system secretin TraK traK
MKJ05_RS23925 (MKJ05_23925) 63865..64326 + 462 WP_000521240 plasmid transfer protein HtdO -
MKJ05_RS23930 (MKJ05_23930) 64316..65671 + 1356 WP_000351841 IncHI-type conjugal transfer protein TrhB traB
MKJ05_RS23935 (MKJ05_23935) 65679..66161 + 483 WP_000377633 hypothetical protein -
MKJ05_RS23940 (MKJ05_23940) 66280..67032 + 753 WP_183079335 protein-disulfide isomerase HtdT -
MKJ05_RS23945 (MKJ05_23945) 67042..67992 + 951 WP_001022587 IncHI-type conjugal transfer lipoprotein TrhV traV
MKJ05_RS23950 (MKJ05_23950) 68001..70682 + 2682 WP_000387412 TraC family protein virb4

Host bacterium

ID   20579 GenBank   NZ_CP113164
Plasmid name   pLBA3-1 Incompatibility group   IncHI2
Plasmid size   237284 bp Coordinate of oriT [Strand]   224808..225061 [-]
Host baterium   Citrobacter braakii strain LBA3

Cargo genes

Drug resistance gene   mph(A), msr(E), mph(E), floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, aph(4)-Ia, aac(3)-IVa
Virulence gene   -
Metal resistance gene   terW, terZ, terA, terB, terC, terD, terE, merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -